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WASHINGTON — President Bush on Tuesday signed into law the last of the fiscal 2009 defense budget bills, finalizing plans for a 3.9 percent pay raise for troops and civilian defense employees starting Jan. 1.

The legislation, approved by Congress last month, sets spending priorities and updates defense policies for fiscal 2009, which began Oct. 1.

Lawmakers passed the defense authorization legislation as a stand-alone bill but approved the $487.7 billion appropriations bill — which actually assigns the money the Pentagon will receive — as part of a massive omnibus spending bill which also allows other government departments to continue fiscal 2008 spending until March.

Under the two bills, active-duty troops and Defense Department civilian workers will receive a 3.9 percent pay boost, the highest increase since 2004. The raise will total about $70 a month for an E-3 with four years of service, and just over $105 a month for an E-5 with 10 years of service.

The measures reauthorize nearly 30 specialty pays and bonuses, including an additional $500 a month for troops kept past their expected separation date by the Defense Department’s stop-loss policy.

Congress also approved a pilot program to give selected servicemembers a three-year hiatus from military service to pursue college courses or professional development then return to the ranks.

Details of the program, which would be open to 20 enlisted troops and 20 officers from each service, still have to be worked out by the Pentagon. But lawmakers wrote the pilot is needed to “evaluate the need for more flexibility in career patterns” as officials look ahead at recruiting and retention challenges.

Other provisions require closer examination of military contracts and the creation of a database of problem contractors: one who overcharge the government or use improper business practices.

But lawmakers dropped a provision in the legislation to bar contractors in combat zones from performing some sensitive jobs, such as detainee interrogations, after the White House threatened a veto of the authorization bill.

The budget funds Pentagon plans to expand number of troops in the ranks in fiscal 2009, increasing the size of the Army by 7,000, the Marine Corps by 5,000, the Navy by 1,023 and the Air Force by 450.

The appropriations bill does not contain direct funding for ongoing operations in Iraq or Afghanistan. Lawmakers said that additional money will be handled in a supplemental budget request later this year or early in 2009.

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