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FBI Director Robert Mueller on Monday raised significant concerns about requiring military custody for captured suspected terrorists, arguing that the divisive provision in a sweeping defense bill could harm ongoing terrorism investigations.

In a letter to lawmakers, Mueller detailed his concerns with the provision that mandates military custody of a suspect deemed to be a member of al Qaeda or its affiliates and involved in plotting or committing attacks on the United States. The White House has threatened a veto over the language in the bill and limits on the administration's ability to transfer suspected terrorists.

"Because the proposed legislation applies to certain persons detained in the United States, the legislation may adversely impact our ability to continue ongoing international terrorism investigations before or after arrest, derive intelligence from those investigations and may raise extraneous issues in any future prosecution of a person covered" by the provision, Mueller wrote.

The FBI director said the legislation would add a substantial amount of uncertainty as to what steps should be followed in a terrorism investigation in the United States. Mueller also said the provision could restrict the FBI from using a grand jury to gather records or subpoenaing witnesses.

"The legislation ... will inhibit our ability to convince covered arrestees to cooperate immediately, and provide critical intelligence," Mueller said.

Proponents of the provision have defended the legislation, pointing out that it includes a waiver that allows the administration to decide a suspect's fate as well as who should be covered by the requirement.

In an op-ed Monday in The Washington Post, Armed Services Chairman Sen. Carl Levin, D-Mich., and the panel's top Republican, Arizona's John McCain, wrote that the bill's provisions on detainees "represent a careful, bipartisan effort to provide the executive branch the clear authority, tools and flexibility of action it needs to defend us against the threat posed by al Qaeda."

Mueller described the waiver as too cumbersome, requiring that it be obtained from the defense secretary in consultation with the secretary of state and the director of National Intelligence with a certification to Congress.

"These limited exceptions ... fail to recognize the reality of a counterterrorism investigation," Mueller wrote. "Building rapport with, and convincing a covered individual to cooperate once arrested, is a delicate and time-sensitive skill that transcends any one interrogation session."

The Senate resumed work on the massive defense bill Monday and approved an amendment to expand the Joint Chiefs of Staff to include the head of the National Guard. The voice vote approval reflected the overwhelming support for the amendment by Sens. Patrick Leahy, D-Vt., and Lindsey Graham, R-S.C., who had some 70 co-sponsors for their effort.

The head of the National Guard represents 465,000 members of the Army and Air National Guard. In a post-Sept. 11 world, their role has changed dramatically with significant numbers of guardsmen and reservists seeing combat in Iraq and Afghanistan.

"Today's National Guard is a superb 21st Century force trapped inside the 20th Century Pentagon bureaucracy," Leahy said.

The chairman of the Joint Chiefs and the head of the services opposed the move. Army Gen. Martin Dempsey, chairman of the Joint Chiefs, said it could create the impression of inequity because while each service has a reserve component, only the Army and Air Force have a National Guard. Dempsey also testified earlier this month that each chief is subject to civilian oversight with a service secretary. The National Guard does not have a similar arrangement.

The dispute over the detention policy loomed large. Not only has it drawn a veto threat, but the provision has divided senior Senate Democrats, pitting Levin against leaders of the Intelligence and Judiciary committees.

Congress and the administration have been at odds since Obama took office over how to handle captured terror suspects. The administration insists that lawmakers are trying to limit the military, law enforcement and intelligence agents after they've succeeded in killing Osama bin Laden and Anwar al-Awlaki, delivering two body blows to al-Qaida.

Director of National Intelligence James Clapper, in a letter to Sen. Dianne Feinstein, D-Calif., the head of the Intelligence committee, has said the limits in the bill "could deny our nation the ability to respond flexibly and appropriately to unfolding events, including the capture of terrorism suspects."

Republicans counter that their efforts are necessary to respond to an evolving, post-Sept. 11 threat, holding captured terror suspects at the U.S. prison at Guantanamo Bay, Cuba, and trying them by military commissions. In a not-in-my-backyard argument, lawmakers have resisted transferring suspects to the United States.

The sweeping defense bill would authorize $662 billion for military personnel, weapons systems, the wars in Iraq and Afghanistan and national security programs in the Energy Department. Reflecting a period of austerity and deficit-driven cuts in military spending, the bill is $27 billion less than what Obama requested for the fiscal year beginning Oct. 1 of this year.