Sen. Carl Levin (D-Mich.), left, the chairman of the Armed Services Committee, and Sen. John McCain (R-Ariz.), the panel’s ranking minority member. (J. Scott Applewhite — Associated Press)

Before the holiday break, the Senate Armed Services Committee crafted what it saw as compromise legislation that would allow detainees to be held in either civilian or military custody. The legislation would, as backers had originally envisioned, require military custody for al-Qaeda suspects who participate in the planning or execution of attacks against the United States. But it would also provide the administration with a waiver to hold those suspects in civilian custody if it determines that doing so would best serve U.S. national security interests.

Two days after the new measures were unveiled, however, the administration threatened to veto, as a result of the provisions, part of the 2012 National Defense Authorization Act.

Now, Capitol Hill is set for yet another clash over detainees.

For the administration, the legislation is troubling in part because it could apply to suspects in the United States and in part because it could complicate the decision-making process during investigations — effectively whether military or civilian authorities have control.

On Monday, the chairman and the ranking minority members of the Armed Services Committee sought to re-frame the proposal as a balanced approach to an issue that has repeatedly tangled lawmakers, the administration and rights groups.

Sens. Carl Levin (D-Mich.) and John McCain (R-Ariz.) said the administration will still have “broad authority to decide who is covered by this provision and how and when such a decision is made.”

“We are concerned that much of the debate over these provisions demonstrates a basic misunderstanding of what this bill would do and attributes to it many things that it would not do,” the senators wrote in The Washington Post.

There’s little indication, however, that such arguments will win over skeptics, including some Democrats. Sen. Dianne Feinstein (D-Calif.), the chairwoman of the Intelligence Committee, has been a leading opponent of the detainee provisions. Last week, the director of national intelligence, James Clapper, joined the White House in criticizing the legislation, saying it could make it more difficult to handle terrorism cases if there was ambiguity over who had responsibility for individual suspects.

The Justice Department is also registering its concerns about bureaucratic requirement imposed by the legislation. “Agents and prosecutors should not have to spend their time worrying about citizenship status and whether and how to get a waiver signed by the Secretary of Defense in order to thwart an al-Qaeda plot against the homeland,” Lisa Monaco, assistant attorney general for national security, said Monday in a statement.

Civil rights advocates and human rights groups fear the legislation takes a post-Sept. 11 authority that already exists — the use of the military to detain and try suspects — and makes it both permanent and worldwide. The legislation, they say, threatens to roll back the protections provided by a civilian legal system.

The waiver, they say, doesn’t make the legislation palatable.

“The sponsors of [the bill] keep arguing that the waiver makes it okay, that although it’s a very extreme provision, it doesn’t actually have to be followed,” said Christopher Anders, senior legislative counsel for the American Civil Liberties Union. “That doesn’t seem to be a solution.”

The Senate is expected to take up the legislation on the floor later Monday.