Maritime Appropriation Authorization Act for Fiscal Years 1989 and 1990

Maritime Appropriation Authorization Act for Fiscal Years 1989 and 1990 - Authorizes appropriations without fiscal year limitation, as the appropriation Act may provide for the use of the Department of Transportation, for FY 1989 and 1990 for: (1) payment of operating-differential subsidy obligations; (2) operations and training activities; and (3) necessary expenses to acquire and maintain a surge shipping capability in the National Defense Reserve Fleet in an advanced state of readiness.

Amends the Merchant Marine Act, 1936 to terminate on September 30, 1988, the authority of the Secretary of Commerce to enter into a new commitment to guarantee the payment of the interest on, and the unpaid balance of the principal of, any obligation which is eligible to be guaranteed under provisions relating to Federal ship mortgage insurance.

Changes from $100,000 to $400,000 the cap on payments for the maintenance and support of State maritime academies meeting certain requirements. Requires the academies, as a condition to receiving payments or the use of vessels, to require each U.S. citizen entering the academy in a merchant marine officer preparation program, as a condition for graduation, to: (1) pass the Coast Guard merchant marine officer license examination; and (2) agree to serve in a reserve unit of a U.S. armed force for at least six years. Terminates on September 30, 1988, the authority of the Secretary of Transportation to enter into State maritime academy student incentive payment agreements.

Provides that certain petitions relating to bankruptcy and applications relating to protection of securities investors, when brought by the Secretary of Transportation under the Ship Mortgage Act, 1920 do not, in certain circumstances, act as a stay of specified proceedings. (Current law refers to petitions and applications brought but not to petitions and applications to be brought by the Secretary.) Declares that the rights of the Secretary shall not be affected or enjoined by any court.