“The bill attempts to micromanage [the Defense Department] by impeding the Department’s ability to respond to changing circumstances, directing overly prescriptive organizational changes, preventing the closure of Guantanamo, and limiting U.S. engagement with Cuba, and includes provisions that set an arbitrary limit on the size of the President’s National Security Council staff,” OMB said in its assessment of the bill.

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The administration threatened last month to veto the House version of the bill, citing lawmakers’ steps to boost defense funding despite budget caps. Obama vetoed the original version of last year’s bill, only his fifth veto since he took office in 2009, but he later signed an amended version into law.

Sen. John McCain (R-Ariz.), who chairs the Senate Armed Services Committee, opened debate of the bill on the Senate floor on Monday by saying the bill’s effort to reorganize the Pentagon bureaucracy would increase innovation and streamline management of complex security issues. Among other steps, the legislation would do away with a senior office overseeing defense procurement, which some lawmakers see as ineffective.

The OMB singled out 65 provisions as objectionable, starting with the steps that would impede the president’s effort to close the military prison at Guantanamo Bay, in part by linking resettlement of detainees overseas to State Department travel warnings about those countries. Obama has transferred 158 detainees out of Guantanamo since taking office, and he hopes that moving dozens more this year would make it easier to deliver on his long-standing goal of shuttering the prison. The House bill also includes measures to restrict the administration’s ability to resettle inmates overseas.

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The White House also objects to measures in both the House and Senate bills that would cap the number of staff on the president’s National Security Council. The Senate bill limits the number to 150, compared with 100 in the House version, excluding “wholly … administrative” employees.

The NSC has grown exponentially under various administrations in recent decades, doubling from 100 under Bill Clinton to 200 under George W. Bush. Obama’s national security staff numbers about 400, a total that even National Security Adviser Susan E. Rice has said is probably too big. The size has been sharply criticized by Republicans and by some of Obama’s former Cabinet secretaries. They accuse the NSC of “micromanaging” policy and usurping functions of the State and Defense Departments.

Rice has cut the staff by 12 percent over the past 18 months, according to the veto statement, which called the Senate cuts “arbitrary” and liable to inhibit the president’s ability to carry out his “national security and foreign policy agenda in an increasingly complicated world.” In addition to forcing deeper cuts, the House bill said that any increase in the NSC staff above 100, including employees detailed from other agencies, would trigger a provision requiring congressional confirmation of the president’s national security adviser.

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The White House also rejected a provision in the Senate bill that restricts military-to-military interactions with Cuba unless the defense decretary certifies that Havana has stopped human-rights abuses and persecution of dissidents and “members of faith-based organizations.” It also requires Cuba to end all demands for the return of Guantanamo. There is a similar provision in the House bill.

Existing cooperation with Cuba on counter-narcotics, humanitarian relief and other matters has increased since diplomatic relations were reestablished last year. The proposed restriction, which also apparently would end monthly meetings between the U.S. commander of the Guantanamo base and his Cuban counterpart, “would hamper pragmatic, expert-level coordination” between the two governments “on issues that benefit the United States,” the administration said.

At the core of disagreement over recent defense legislation has been the overall level of U.S. military spending. While the Senate version of the bill does not take the same approach as the House bill, which would allocate wartime funding to the base budget, McCain is now backing an amendment that boosts defense spending beyond budget caps.

“This year’s defense budget is more than $150 billion less than fiscal year 2011. And despite periodic relief from the budget caps that imposed these cuts … each of our military services remains underfunded, undersized, and unready to meet current and future threats,” McCain said on the Senate floor this week.