The House of Representatives is set to vote on a new defense bill that would require terrorist suspects to remain in military custody.
The $662 billion measure, known as the National Defense Authorization Act, authorizes funds for the U.S. military, weapons, national security and the wars in Iraq and Afghanistan.
The bill would require suspected al Qaeda terrorists to be in military custody for indefinite periods of time, even if they aren't awaiting trial. The measure would also apply to U.S. citizens linked to the terrorist group.
Before the vote, FBI Director Robert Mueller expressed his "uncertainty" about the new provisions.
He said requiring military custody could interfere with FBI investigations and the ability to interrogate terrorist suspects.
"(The bill) talks about not interrupting interrogations, which is good, but gaining cooperation is something different than continuing an interrogation," Mueller said.
"Given the statute the way it is now, it does not give me a clear path to certainty as to what is going to happen when arrests are made in a particular case," he added. "The possibility looms that we will lose opportunities to obtain cooperation from the persons in the past that we've been fairly successful in gaining."
The legislation is expected to pass the House and head to the Senate Thursday.
The White House has threatened to veto the measure because the requirement denies flexibility in fighting terrorism.