by Charlie Savage (New York Times)

WASHINGTON — Defying the Obama administration’s threat of a veto, the Senate on Tuesday voted to increase the role of the military in imprisoning suspected members of Al Qaeda and its allies — including people arrested inside the United States.

By a vote of 61 to 37, the Senate turned back an effort to strip a major military bill of a set of disputed provisions affecting the handling of terrorism cases. While the legislation still has several steps to go, the vote makes it likely that Congress will eventually send to President Obama’s desk a bill that contains detainee-related provisions his national-security team has said are unacceptable.

The most disputed provision would require the government to place into military custody any suspected member of Al Qaeda or one of its allies connected to a plot against the United States or its allies. The provision would exempt American citizens, but would otherwise extend to arrests on United States soil. The executive branch could issue a waiver and keep such a prisoner in the civilian system.

A related provision would create a federal statute saying the government has the legal authority to keep people suspected of terrorism in military custody, indefinitely and without trial. It contains no exception for American citizens. It is intended to bolster the authorization to use military force against the perpetrators of the terrorist attacks of Sept. 11, 2001, which lawmakers enacted a decade ago.

The administration has strongly opposed the mandatory military custody provision, saying it “would raise serious and unsettled legal questions and would be inconsistent with the fundamental American principle that our military does not patrol our streets.”

In recent days, several top national security officials — including the secretary of defense, Leon E. Panetta; the director of national intelligence, James R. Clapper; and the director of the Federal Bureau of Investigation, Robert S. Mueller III, have voiced opposition to the proposal, as have several former counterterrorism officials from the Bush administration.

But among Republican senators, there was nearly unanimous support for keeping the detainee provisions in the bill: 44 Republicans voted for them, while two — Mark Kirk of Illinois and Rand Paul of Kentucky — voted to remove them.

By contrast, members of the Democratic caucus were deeply divided: 35 wanted to strip the detainee provisions from the bill, but 17 voted to keep them in it. About half of the Democrats who supported keeping the provisions were members of the Senate Armed Services Committee, whose chairman, Carl Levin of Michigan, shaped the package with Republicans.

“We are at war with Al Qaeda, and people who are determined to be part of Al Qaeda should be treated as people who are at war with us,” Mr. Levin said in the debate leading up to the vote.

Mr. Levin also said that he supported the use of civilian trials for some terrorism cases and said that the waiver in the bill would leave that option available to the administration. And he repeatedly quoted from a 2004 Supreme Court case approving the detention without trial of an American citizen captured in Afghanistan and accused of fighting with the Taliban.

Senator Mark Udall, a Colorado Democrat and a member of the Armed Services Committee who sponsored the unsuccessful proposal to strip the detainee proposals from the bill, warned that the provisions could “destabilize” counterterrorism efforts, “open the door to domestic military police powers and possibly deny U.S. citizens their due process rights.” He argued that lawmakers should slow down and revisit the issue later.

Senator Lindsey Graham, Republican of South Carolina, said that the time had come for Congress to enact a statutory framework for how terrorism cases should be handled.

Mr. Graham also argued that detaining a terrorist for the purpose of interrogating him about planned attacks — even on domestic soil — should be viewed as a wartime act, not an exercise of “police” power that should raise any concerns about the military taking over law enforcement functions.

“I don’t believe fighting Al Qaeda is a law enforcement function,” Mr. Graham said. “I believe our military should be deeply involved in fighting these guys at home or abroad.”

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