"Right now the president has a choice of whether the FBI or the military should take custody of a terror suspect, and there's often a preference for giving the FBI first dibs because of their expertise in interrogation and intelligence-gathering," said Raha Wala, an analyst for Human Rights First. "This would take away that choice and require the military to take custody of a huge category of terrorism suspects captured at home or abroad, which I think is very alarming."

The provision was inserted into the NDAA at the request of Sen. John McCain, R-Ariz., ranking member of the Senate Armed Services Committee, according to Senate aides familiar with the panel's deliberations. McCain has long been a proponent of putting terrorism suspects into military custody and trying them before military commissions rather than in civilian courts.

Like many of his fellow Republicans, McCain fiercely criticized the Obama administration for having FBI agents detain and question would-be bomber Umar Farouq Abdulmuttalab, who attempted to blow up a packed airliner on Christmas Day 2009.

"That person should be tried as an enemy combatant; he's a terrorist," McCain said on CNN in January 2010. "To have a person be able to get lawyered up when we need that information very badly betrays or contradicts the president's view that we are at war."

Rachael Dean, a spokeswoman for McCain, declined repeated requests in recent weeks to comment on the lawmaker's support for the new provision.

The measure seems certain to reignite the heated political debate over the Obama administration's detention policies. Obama recently reversed his campaign pledge to close down the Guantanamo Bay detention facility and instead acknowledged that it will continue to hold terror suspects indefinitely. Obama also reversed an earlier vow to try Sept. 11 mastermind Khalid Sheikh Mohammed in a civilian court.

Despite those shifts, many Republicans argue that the president is soft on terror because of his stated preference for having FBI agents take custody of terror suspects and for trying militants in civilian courts whenever possible. Republicans were particularly incensed that FBI agents read Farouk his Miranda rights and gave him access to a lawyer. Sen. Susan Collins, a moderate Republican from Maine, said in January 2010 that the Obama administration had made a serious mistake by treating "a foreign terrorist who had tried to murder hundreds of people as if he were a common criminal."

Beyond the political wrangling, many legal experts believe the new measure would significantly change the legal contours of the broader war on terror.

Benjamin Wittes, a senior fellow at the Brookings Institution, argued in a recent essay that such a change could be "profoundly disruptive" to American counterterrorism efforts. Wittes noted that a suspect arrested by the FBI in the midst of an unfolding terrorist plot would have to be transferred to military custody even if the militant was providing useful information about the planned attack, potentially setting back the investigation significantly.