Coast Guard and Maritime Transportation Act of 2006 - Title I: Authorization - (Sec. 101) Authorizes appropriations for FY2006 for the Coast Guard (CG) for: (1) CG operation and maintenance, with a portion from the Oil Spill Liability Trust Fund for certain purposes under the Oil Pollution Act of 1990 (OPA purposes); (2) acquisition, construction, rebuilding, and improvement of aids to navigation, shore and offshore facilities, vessels, and aircraft, including related equipment (earmarking a Fund amount for OPA purposes, for the Integrated Deepwater Systems, and for sustainment of legacy vessels and aircraft); (3) CG research, development, test, and evaluation of technologies, materials, and human factors directly relating to improving CG performance in search and rescue, aids to navigation, marine safety, marine environmental protection, enforcement of laws and treaties, ice operations, oceanographic research, and defense readiness, with a portion from the Fund for OPA purposes; (4) retired pay, payments under the Retired Serviceman's Family Protection and Survivor Benefit Plans, and payments for medical care of retired personnel and their dependents; (5) alteration or removal of bridges over U.S. navigable waters constituting obstructions to navigation, and for personnel and administrative costs associated with the Bridge Alteration Program; (6) environmental compliance and restoration at CG facilities; and (7) the CG Reserve program, including personnel and training costs, equipment, and services. (Sec. 102) Authorizes a CG end-of-strength of 45,500 active duty military personnel for FY2006. Authorizes average military training student loads for FY2006 in specified numbers under the categories of Recruit/Special, Flight, Professional, and Officer. (Sec. 103) Authorizes additional appropriations to the CG for non-reimbursed expenditures related to Hurricane Katrina for: (1) operation and maintenance of the CG, including search and rescue, clearing channels, emergency response to oil and chemical spills, and higher fuel costs; and (2) the acquisition, construction, renovation, and improvement of aids to navigation, shore and offshore facilities, and vessels and aircraft, and equipment due to damage caused by such storm. (Sec. 104) Authorizes appropriations for FY2006 and FY2007 for the CG to continue deployment of a web-based risk management system to help reduce accidents and fatalities. Title II: Coast Guard - (Sec. 201) Amends federal naval law to extend the authority of the Secretary of the department in which the Coast Guard is operating (Secretary) to control the anchorage and movement of vessels to ensure the safety or security of U.S. naval vessels in U.S. navigable waters to include all waters of the U.S. territorial sea as described in Presidential Proclamation No. 5928 of December 27, 1988. (Sec. 202) Authorizes the Commandant of the CG (in coordination with the Secretary of State) to provide in conjunction with regular CG operations technical assistance, including law enforcement and maritime safety and security training, to foreign navies, coast guards, and other maritime authorities. (Sec. 203) Revises CG officer promotion eligibility requirements to authorize the Secretary to waive certain ones to allow CG officers to have at least two opportunities for consideration for promotion to the next higher grade as officers below the promotion zone. (Sec. 204) Revises requirements for appointment of the director of the CG Band to authorize the Secretary to designate as director any individual determined to possess the necessary qualifications. (Currently the Secretary is required to designate the director from among qualified members of the CG.) Authorizes the current CG Band Director, upon enactment of this Act, to be promoted immediately to a commissioned grade, not to exceed captain, as determined by the Secretary to be most appropriate to the individual's qualifications and experience. (Sec. 205) Authorizes the Secretary to use one-step turnkey selection procedures when entering into contracts for the design and construction of CG facilities. Defines "one-step turnkey selection procedures" to mean procedures used for the selection of a contractor on the basis of price and other evaluation criteria to perform, in accordance with a firm fixed-price contract, both the design and construction of a facility using performance specifications supplied by the Secretary. (Sec. 206) Authorizes the Secretary, during an act of terrorism or transportation security incident, to order CG Ready Reserve members to active duty to no more than 60 days (currently, 30 days) in any four-month period and no more than 120 days (currently, 60 days) in any two-year period. (Sec. 207) Prohibits CG Reserve officers on an active-duty list from being counted as part of the authorized number of officers in the CG Reserve. (Currently, the authorized number of CG Reserve officers in an active status is 5,000.) Revises the distribution method for determining the number of CG Reserve officers on active status that are authorized to be serving in each grade. (Sec. 208) Authorizes the CG, in carrying out its duties as authorized by the Secretary, to utilize any motorized vehicle placed at its disposition by any member of the Auxiliary, by any corporation, partnership, or association, or by any state to tow federal government property. Makes CG appropriations available for payment of motorized vehicles when assigned to CG duty. (Sec. 209) Authorizes the CG Commandant to prescribe regulations for the award of fellowships in CG history to eligible U.S. citizens or nationals. Authorizes the CG Commandant to award up to two fellowships annually, (with fellowships not to exceed $25,000 in any year). (Sec. 210) Directs the Secretary to submit to Congress a plan for: (1) operation and maintenance after FY2006 of the CG polar icebreakers POLAR STAR, POLAR SEA, and HEALY that does not rely on the transfer of funds to the CG by any other federal agency; and (2) long-term recapitalization of such assets. Requires the Secretary to take necessary measures to ensure the CG maintains, at a minimum, its current vessel capacity for carrying out ice breaking in the Arctic and Antarctic, Great Lakes, and New England regions until it has implemented the long-term recapitalization of such vessels. Declares that nothing in this section shall preclude the Secretary from seeking reimbursement for vessel operation and maintenance costs from other federal agencies, including foreign countries, that benefit from the use of such vessels. (Sec. 211) Provides that the CG shall operate as a service in the Navy upon a declaration of war (current law), but only if Congress so directs in the declaration. Maintains the President's authority to direct the CG to operate as a service in the Navy. (Sec. 212) Prohibits the CG Commandant from moving CG personnel, property, or other assets to the West Campus of St. Elisabeth's Hospital until the Administrator of General Services submits a plan to Congress that includes providing for, among other things: (1) road access to the site from Interstate Route 295; and (2) the design of facilities for at least one federal agency other than the CG that would house no less than 2,000 employees. (Sec. 213) Directs the Secretary to report to Congress on opportunities for, and the feasibility of, co-locating CG assets and personnel at facilities of other armed forces throughout the United States. (Sec. 214) Directs the Secretary to examine the technical feasibility of using bio-diesel fuel in new and existing CG vehicles and vessels, with emphasis on the use of such fuel in ports with high-density vessel traffic, including ports for which vessel traffic systems have been established. (Sec. 215) Provides that the initial appointment of the Director of the Boating Safety Office shall be in the grade of Captain. (Sec. 216) Directs the Secretary to provide to Congress a proposal and cost analysis for construction of an enclosed hangar at Air Station Barbers Point, Hawaii. (Sec. 217) Authorizes the President to appoint directly permanent commissioned officers in the Regular CG in grades of ensign through lieutenant from among specified categories. (Currently, all appointments for officers in grades of ensign or above must be by and with the advice and consent of the Senate.) Retains the requirement for the advice and consent of the Senate for presidential appointments in grades of lieutenant commander and above. Extends the same requirements to wartime temporary service promotion. (Sec. 218) Amends federal armed forces law to redesignate CG law specialists as judge advocates. Title III: Shipping and Navigation - (Sec. 301) Defines "ferry" as a vessel used on a regular schedule that provides transportation only between places that are not more than 300 miles apart to passengers or vehicles (including railroad cars) that are being used, or have been used, in transporting passengers or goods. Treats certain passenger and small passenger vessels carrying passengers with (current law) or without charge as ferries and under the merchant marine jurisdiction of the Secretary. (Sec. 302) Requires the Secretary to establish: (1) establish new pilotage rates for the Great Lakes before March 1 of each year; (2) base pilotage rates by a full ratemaking at least once every five years and conduct annual reviews of, including make adjustments to, such rates in each intervening year. Requires the assignment of a sufficient number of individuals to process pilot registration applications. (Sec. 303) Amends the Maritime Drug Law Enforcement Act with respect to vessel drug smuggling cases to provide that the response of a foreign nation to a claim of registry (in cases where the vessel is without nationality) may be made by radio, telephone, or similar oral or electronic means, and is conclusively proved by certification of the Secretary of State (or designee). (Sec. 304) Directs the Secretary of Transportation to develop and implement a program to promote the transportation of liquefied natural gas to the United States on U.S.-flag vessels. Amends the Deepwater Port Act of 1974 to require the Secretary, in order to promote the security of the United States, to give top priority to the processing of a license for liquefied natural gas facilities at a deepwater port that will be supplied with such gas by U.S.-flag vessels. Requires an application for such license to include, among other things, the nation of registry for, and the nationality or citizenship of officers and crew serving on board, vessels transporting natural gas to a deepwater port. Requires the Secretary to report to Congress on implementation of this section. (Sec. 305) Amends federal shipping law to authorize the Secretary to use maritime safety and security teams to implement any CG mission. (Sec. 306) Amends the Coast Guard and Maritime Transportation Security Act of 2004 to set forth civil penalties for continuing violations of such Act. (Sec. 307) Amends the Merchant Marine Act, 1936 to authorize the Secretary to provide for the training of U.S. Merchant Marine Academy cadets on any vessel considered necessary or appropriate or in the national interest. (Sec. 308) Authorizes the Secretary of Transportation to require mortgagees of documented vessels to submit reports in any reasonable form and manner the Secretary may prescribe to ensure compliance with laws governing the qualifications of vessels to engage in the coastwise trade and the fisheries. (Sec. 309) Amends federal shipping law to establish an appeal process for individuals who have been found ineligible and denied a waiver for the issuance of a transportation security card. (Sec. 310) Authorizes only vessels with certificates of documentation with a registry endorsement to engage in: (1) the setting, relocation, or recovery of anchors or other mooring equipment of a mobile offshore drilling unit located over the outer Continental Shelf; or (2) the transportation of merchandise or personnel to or from a point in the United States from or to a mobile offshore drilling unit located over the outer Continental Shelf that is not attached to the seabed. (Sec. 311) Exempts from CG inspection requirements Aleutian trade vessels that are not more than 2,500 gross tons. (Sec. 312) Requires operators of certain freight vessels to ensure: (1) each riding gang member on the vessel is a U.S. citizen, an alien lawfully admitted to the United States for permanent residence, or possesses a U.S. nonimmigrant visa; (2) all required documentation for each member is kept on the vessel for inspection; (3) each member is on the crew list; and (4) a background check has been done on such member. Limits the type of work and the number of workdays for non-U.S. citizen or resident riding gang members. Sets forth civil penalties for employment of non-U.S. citizen or resident riding gang members. Title IV: Miscellaneous - (Sec. 401) Establishes a junior reserve officers training program in cooperation with the Camden County High School in Camden County, North Carolina. (Sec. 402) Amends the Coast Guard and Maritime Transportation Act of 2004 to authorize the CG Commandant to convey all right, title, and interest of the United States in the CG Cutter PLANETREE to the CAS Foundation, Inc., in Indiana. Requires the recipient of such vessel to use it for only humanitarian purposes. (Sec. 403) Authorizes appropriations to the Department of Transportation (DOT) for capital expenses related to the LORAN-C navigation infrastructure for FY2006 and FY2007. Authorizes the Secretary of Transportation to transfer from the Federal Aviation Administration (FAA) and other DOT agencies funds appropriated under this section to reimburse the CG for related expenses. (Sec. 404) Directs the Secretary to conduct a three-year pilot program for the long-range tracking of vessels by satellite to aid maritime security and response to maritime emergencies. Authorizes appropriations for FY2006-FY2008. (Sec. 405) Directs the CG to continue cooperative agreements and partnerships with organizations that provide marine vessel safety training and cold water immersion education and outreach programs for fishermen and children. (Sec. 406) Directs the CG Commandant to review and report to Congress on the adequacy of certain CG assets and strength of active duty personnel to carry out CG missions, including search and rescue, illegal drug and migrant interdiction, aids to navigation, ports, waterways and coastal security, marine environmental protection, and fisheries law enforcement. (Sec. 407) Directs the CG Commandant, upon the decommissioning of the CG Cutter MACKINAW, to convey all right, title, and interest of the United States in and to it to the Icebreaker Mackinaw Maritime Museum, Inc., in Michigan, (recipient), if the recipient meets specified conditions, including that it: (1) use the vessel for purposes of a museum; (2) hold the federal government harmless for claims arising from exposure to asbestos and other hazardous materials after the conveyance; and (3) have funds available to operate and maintain the vessel in good working condition. (Sec. 408) Directs the Secretary to report to Congress on: (1) the implementation of the Integrated Deepwater Systems Program; and (2) the acceleration of of the current Deepwater Program acquisition timeline that reflects its completion in each of 10 years and 15 years. Directs the CG Commandant to report to Congress on the status of the CG's implementation of the Government Accountability Office's (GAO) recommendations in its report, GAO-04-380, entitled "Coast Guard Deepwater Program Needs Increased Attention to Management and Contractor Oversight." (Sec. 409) Directs the Secretary to study and report to Congress on the potential impact on CG acquisitions that require the CG to acquire only U.S.-constructed helicopters. (Sec. 410) Directs the Administrator of the Environmental Protection Agency (EPA) to study and report to Congress on public health and safety concerns related to the pollution of Newtown Creek, New York City, New York, caused by seepage of oil into Newtown Creek from underground oil spills in Greenpoint, Brooklyn, New York. (Sec. 411) Directs the CG Commandant to report to Congress on the effectiveness, and costs associated with, implementing at all Sector Command Centers, Joint Harbor Operations Centers, and strategic defense and energy dependent ports software information systems technology (specifically the software being tested at Joint Harbor Operations Centers) that can identify inbound vessels and shippers and their cargo for potential threats to national security before they reach U.S. ports. (Sec. 412) Authorizes appropriations to the Maritime Administration to carry out an assessment of, and planning for, the impact of an Arctic Sea Route on the Alaskan people. (Sec. 413) Directs the CG Commandant to study and report to Congress on the current homeport arrangement of the CG polar icebreaker HEALY to determine whether an alternative arrangement would enhance the CG's capabilities to carry out the recommendation to maintain year-round icebreaker capability for the Arctic that was included in the National Academy of Sciences' report entitled "Polar Icebreaker Roles and U.S. Future Needs: A Preliminary Assessment (ISBN: 0-309-10069-0)." (Sec. 414) Requires Commandant of the Coast Guard, in reviewing a lease, easement, or right-of-way for an offshore wind energy facility in Nantucket Sound under the Outer Continental Shelf Lands Act, not later than 60 days before the date established by the Secretary of the Interior for publication of a draft environmental impact statement, to specify the reasonable terms and conditions the Commandant determines to be necessary to provide for navigational safety with respect to the proposed lease, easement, or right-of-way and each alternative to the proposed lease, easement, or right-of-way considered by the Secretary. Requires, in the granting of such a lease, easement, or right-of-way for such a facility, the Secretary to incorporate in the lease, easement, or right-of-way reasonable terms and conditions the Commandant determines to be necessary to provide for navigational safety. (Sec. 415) Prohibits the Secretary, acting through the CG Commandant, from approving the security plan for a liquefied natural gas import facility at Port Richmond in Philadelphia, Pennsylvania, until the Secretary conducts a vulnerability assessment. (Sec. 416) Amends the Magnuson-Stevens Fishery Conservation and Management Act to revise the Alaska and western Pacific community development programs to establish the western Alaska community development quota program (effectively, replaces the Alaska and western Pacific community development program) to allocate to eligible western Alaska villages an annual percentage of total allowable catch, harvest level, or other annual catch limit from fisheries in the Bearing Sea and Aleutian Islands Management Area. Establishes a community development quota program panel to administer the program. (Sec. 417) Revises crab quota share allocations under the Voluntary Three-Pie Cooperative Program for certain crab fisheries of the Bering Sea and Aleutian Islands. (Sec. 418) Authorizes certain vessels constructed in Canada to transport fish or shellfish between places in the State of Maine if: (1) the vessel transported fish or shellfish between such places before January 1, 2005; (2) before January 1, 2005, the owner of the vessel transported fish or shellfish pursuant to a valid wholesale seafood license; (3) the vessel is owned by an individual meeting certain citizenship requirements; and (4) the owner of the vessel submits to the Secretary an affidavit certifying that all requirements have been met. (Sec. 419) Authorizes the Secretary to transfer $1 million to the National Telecommunications and Information Administration of the Department of Commerce to award a competitive grant to develop a device that integrates a Class B Automatic Identification System (AIS) transponder (International Electromechanical Commission standard 62287) with an Federal Communications Commission (FCC) approved wireless maritime data device to enable such device to provide wireless maritime data services. Expresses the sense of the Senate that the FCC should resolve within 60 days after enactment of this Act the disposition of its rulemaking on the AIS and licensee use of specified frequency bands (RM-10821, WT Docket Number 04-344). (Sec. 420) Directs the Secretary to study and report to Congress on: (1) the carriage of a voyage data recorder by a passenger vessel that carries more than 399 passengers; and (2) standards for voyage data recorders use. (Sec. 421) Authorizes U.S. purse seine fishing vessels transiting to or from, or fishing exclusively for highly migratory species in, the treaty area under a fishing license issued pursuant to the 1987 Treaty of Fisheries Between the Governments of Certain Pacific Islands States and the Government of the United States of America to engage foreign citizens to meet manning requirements for a 48 month period, if no U.S. citizen personnel are readily available. Requires a report to Congress on purse seine fishing vessels. Title V: Lighthouses - (Sec. 501) Transfers administrative jurisdiction over specified CG lighthouse facilities located on National Forest System lands in the State of Alaska from the Secretary of Agriculture to the Secretary. (Sec. 502) Directs the Secretary to transfer to the Secretary of Agriculture all administrative jurisdiction over the Tree Point Light Station if the Secretary determines that it is no longer needed by the CG. Authorizes the CG Commandant to reserve rights to operate and maintain federal aids to navigation at the site of the lighthouse. Declares that nothing in this section shall affect any responsibilities of the CG Commandant for the remediation of hazardous substances and petroleum contamination at the Tree Point Light Station. (Sec. 503) Describes Cape St. Elias Light Station (as described in the map entitled "Cape St. Elias Light Station," dated September 14, 2004), and Point Wilson Lighthouse, Fort Worden State Park, Washington, for purposes of their conveyance. (Sec. 504) Revokes any reservation of specified public land within the external boundaries of St. Marks National Wildlife Refuge in Wakulla County, Florida, for lighthouse purposes by the Executive Order dated November 12, 1838, as amended by Public Land Order 5655, dated January 9, 1979. Transfers administrative jurisdiction over such land, including all improvements located on it, from the department in which the CG is operating to the Secretary of the Interior, without reimbursement. Grants the CG sole responsibility to fund and conduct any response or restoration action required under federal or state law with respect to the release of any hazardous substance, pollutant, contaminant, petroleum, or petroleum product on such lands. Includes the lands as part of the St. Marks National Wildlife Refuge. Subjects the transfer, and the administration of such lands, to such conditions and restrictions as the Secretary considers necessary to ensure that the CG maintains jurisdiction over navigation functions at St. Marks National Wildlife Refuge. Title VI: Delaware River Protection and Miscellaneous Oil Provisions - Delaware River Protection Act of 2006 - (Sec. 602) Amends the Ports and Waterways Safety Act to require any person who knows of a release from a vessel or facility of any object that creates an obstruction in the navigable waters of the United States to notify the Secretary and the Secretary of the Army. (Sec. 603) Amends the Oil Pollution Act of 1990 to increase liability limits associated with oil spills for single-hull and double-hull tank vessels and nontank vessels. Requires the Secretary to report to Congress on: (1) the extent to which oil discharges from vessels and non-vessel sources result in response costs and damages that exceed such limits; (2) the impact that claims against the Oil Spill Liability Trust Fund that exceed such limits will have on the Fund; and (3) recommendations on whether such limits need to be further adjusted. (Sec. 604) Requires the Philadelphia Area Committee to review and revise annually the Philadelphia Area Contingency Plan (a plan to remove a worst case discharge, and to mitigate or prevent a substantial threat of such a discharge, from a vessel, offshore facility, or onshore facility operating in or near an area) to include available data and biological information on environmentally sensitive areas of the Delaware River and Delaware Bay that has been collected by federal and state surveys. (Sec. 605) Establishes the submerged oil program to detect, monitor, and evaluate the environmental effects of submerged oil in the Delaware River and Bay region. Directs the Commandant of the CG to conduct a demonstration project to develop and demonstrate technologies and management practices to remove submerged oil from the Delaware River and other navigable waters. Authorizes appropriations for FY2006-FY2010. (Sec. 606) Directs the Comptroller General to conduct an assessment of the cost of response activities and claims related to oil spills from vessels that have occurred since January 1, 1990, for which the total costs and claims paid was at least $1 million per spill. (Sec. 607) Establishes the Delaware River and Bay Oil Spill Advisory Committee to make recommendations to the CG Commandant, Governors of New Jersey, Pennsylvania, and Delaware, and Congress on measures to improve the prevention of, and response to, future oil spills in the Delaware River and Delaware Bay. Authorizes appropriations for FY2006 and FY2007. (Sec. 608) Amends the Federal Water Pollution Control Act to redefine "nontank vessel" to include all nontank vessels (not just U.S. nontank vessels) for purposes of requiring such vessels that travel within 12 miles of the United States to have response plans for the discharge of oil. Title VII: Hurricane Response - (Sec. 701) Authorizes the Secretary, subject to availability of appropriations, to reimburse an eligible person for losses to their qualified property due to damage caused by Hurricane Katrina or Hurricane Rita. (Sec. 702) Authorizes the Secretary to extend temporarily the expiration date of merchant mariners' licenses and documents, including any certificate of registry, certificate of inspection or certificate of compliance issued to a vessel, located in Alabama, Mississippi, or Louisiana. (Sec. 704) Authorizes CG members assigned to duty in support of units in the Eighth CG District area to mitigate the consequences of, or assist in the recovery from, Hurricane Katrina during the period from August 28, 2005, to January 1, 2006, and who would lose accumulated leave in excess of 60 days as a result of such assignment, to retain an accumulated total of up to 120 days of leave. (Sec. 705) Requires the Secretary to report to Congress on: (1) the impact of Hurricane Katrina, including, specifically, upon the CG's assets and operations; and (2) navigable waterways. Requires the reports to include assessment of the CG's responses to such impacts. Title VIII: Ocean Commission Recommendations - (Sec. 801) Directs the Secretary to work with responsible officials and agencies of other nations to accelerate efforts at the International Maritime Organization (IMO) to enhance flag state oversight and enforcement of security, environmental, and other agreements adopted by the IMO. (Sec. 802) Directs the Secretary to: (1) undertake outreach programs to educate owners and operators of boats using two-stroke engines about associated pollution; and (2) support voluntary programs that reduce such pollution and encourage the early replacement of older two-stroke engines. (Sec. 803) Directs the Secretary to: (1) integrate vessel monitoring system data into its maritime operations databases to improve monitoring and enforcement of federal fisheries laws; and (2) work with the Undersecretary of Commerce for Oceans and Atmosphere to ensure effective use of such data for monitoring and enforcement. (Sec. 804) Directs the Secretary to report biennially to Congress on steps the CG will take to significantly improve the detection and interdiction of illegal incursions into the U.S. exclusive economic zone by foreign fishing vessels. Title IX: Technical Corrections - (Sec. 901) Makes technical and conforming amendments to various laws related to the CG and maritime transportation.