Maritime Administration Authorization Act for Fiscal Year 2012

Requires the Maritime Administration to assess, and report its findings, conclusions, and recommendations to Congress on, the potential for using container-on-barge transportation on the inland waterways system.

(Sec. 3) Revises the purposes of the short sea transportation program to include promoting more efficient use of the U.S. navigable waters.

(Sec. 4) Amends the Merchant Ship Sales Act of 1946 to allow, with the concurrence of the Secretary of Defense (DOD), the Secretary to use National Defense Reserve Fleet and Ready Reserve Force vessels for civil contingency operations and Maritime Administration promotional and media events when in the best interests of the U.S. government.

(Sec. 5) Authorizes the Secretary to establish a green ships program to identify, evaluate, test, demonstrate, or improve emerging marine technologies and practices likely to achieve environmental improvements by reducing air or water emissions or other ship discharges, increasing fuel economy or use of alternative fuels and alternative energy, or controlling aquatic invasive species.

Authorizes the Secretary to promulgate regulations establishing fees to recover reasonable costs for services rendered by the Secretary and academic, public, and non-governmental entities. Requires such fees to be deposited in a special fund to carry out the activities for which the fees were collected.

Directs the Secretary to report to Congress on the green ships program.

(Sec. 6) Requires the agency head responsible for the administration of U.S. navigation or vessel-inspection laws and the Administrator of the Maritime Administration to certify to Congress of the non-availability of qualified U.S. flag vessels to meet national defense requirements in the event that the agency head considers it in the national interest to waive such laws.

(Sec. 7) Amends the Floyd D. Spence National Defense Authorization Act for Fiscal Year 2001 to direct the Secretary to provide briefings, upon request, to Congress on progress made to recycle National Defense Reserve Fleet vessels.

(Sec. 8) Extends through FY2025 the Maritime Security Fleet Program.

Authorizes the Secretary, subject to the concurrence with the DOD Secretary, to acquire certain Maritime Security Fleet vessels being retired for inclusion in the National Defense Reserve Fleet.

(Sec. 9) Directs the Comptroller General to study, and report the results to Congress on, the training needs of the maritime workforce.

(Sec. 10) Directs the DOT Inspector General to assess: (1) the source selection procedures and practices used to award Maritime Administration's National Defense Reserve Fleet vessel recycling contracts, and (2) the process, procedures, and practices used for the Maritime Administration's qualification of recycling facilities.

(Sec. 11) Prohibits the Administrator of the Maritime Administration and the CG Commandant from receiving, maintaining, dismantling, recycling, or taking any other specified action with respect to the CG's icebreakers Cutter POLAR SEA (WAGB 11) and Cutter POLAR STAR (WAGB 10) until: (1) two years after the appropriate congressional committees receive the polar icebreaker business case analysis for replacing or performing service life extensions on the icebreakers, or (2) the CG has replaced those icebreakers with two "in commission, active" heavy polar icebreakers.

(Sec. 12) Authorizes appropriations to the Secretary for FY2012 for the Maritime Administration for: (1) operations and training activities, including U.S. Merchant Marine Academy capital improvements and maintenance and repair for State Maritime Schools training ships; (2) administrative expenses related to maritime guaranteed loan commitments; and (3) the disposal of non-retention vessels in the National Defense Reserve Fleet.