Grant allocations announced Wednesday represent a 40 percent reduction in urban security funds for New York and Washington.
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State Homeland Security Grant program takes the biggest hit, with a 49 percent reduction.
If supplemental spending bill isn't finished by early July, promotions could be postponed and recruitment efforts suspended.
Bill includes nearly $175 million not requested by the White House.
House spending measure allots $45.6 million more than the Bush administration requested to the consortium.
Last month, department reported that 25 major programs had surpassed original cost estimates by 50 percent.
Attorney General has argued that sharing too many details about NSA surveillance program could diminish its usefulness.
Language passed by House would shift $15 million away from the office implementing the pay-for-performance system.
Ex-NSA chief approved by wide margin.
Air Force program is more than three years behind schedule and will cost $500 million more than originally estimated, GAO says.