Maritime Administration Act for Fiscal Year 2009

(Sec. 5) Requires, subject to appropriations, grants, loans, and loan guarantees to small shipyards for capital improvements and assistance for training programs to foster technical skills and operational productivity in communities with economies related to or dependent on the maritime industry.

(Sec. 6) Allows state maritime academy student incentive payments to be made to the academy or the student. Doubles the level of payments, removes a requirement that the student be attending the academy when payments are made, allows the payments to be used for tuition, and requires recipients to accept midshipman and enlisted reserve (currently, enlisted reserve) status in the U.S. Navy Reserve (including the Merchant Marine Reserve).

(Sec. 7) Extends to December 31, 2015, the expiration of the authority of the Secretary to provide war risk insurance and reinsurance.

(Sec. 8) Conditions the waiver of navigation and inspection laws in the interest of national defense on a determination by the Maritime Administrator that qualified U.S. flag capacity is unavailable to meet national defense requirements.

(Sec. 9) Requires the Coast Guard commandant, acting through the appropriate Area Committee established under certain provisions of the Federal Water Pollution Control Act, to submit to specified congressional committees a vessel traffic risk assessment and related recommendations for Cook Inlet, Alaska, and for the Aleutian Islands, Alaska. Authorizes appropriations.

(Sec. 10) Amends provisions relating to vessels and seamen to exclude from the definition of "fish processing vessel" a fishing vessel operating in Alaskan waters under an Alaskan permit or license that fillets: (1) only salmon taken by that vessel; and (2) less than 5 metric tons of such salmon during any 7-day period.

(Sec. 11) Modifies the circumstances in which at least 50% of the gross tonnage of cargoes transported on ocean vessels and procured, furnished, or financed by the U.S. government must be transported on privately-owned commercial vessels of the United States.

(Sec. 12) Amends the Longshore and Harbor Workers' Compensation Act to modify the definition of "employee" to make it applicable to individuals who are employed to manufacture any recreational vessel under 165 feet in length or are employed to repair any recreational vessel, or to dismantle any part of any recreational vessel in connection with repair of the vessel.

(Sec. 13) Authorizes appropriations to the Secretary of Transportation, for the Maritime Administration, for: (1) operations and training; (2) expenses to maintain and preserve a U.S. flag merchant fleet to serve national security needs; (3) paying reimbursement under specified provisions of the Maritime Security Act of 2003 relating to a maintenance and repair reimbursement pilot program; (4) disposal of obsolete vessels in the National Defense Reserve Fleet; (5) the cost of loan guarantees under provisions relating to direct loans for fisheries; and (6) administrative expenses related to specified programs.