By Jeremy Pelofsky and Laura MacInnis
WASHINGTON (Reuters) - President Barack Obama issued a policy directive on Tuesday making clear that not all al Qaeda suspects would be held in U.S. military custody, fleshing out exceptions allowed under a sweeping defense bill that sought to have the Pentagon prosecute most suspects.
Under the directive, al Qaeda suspects arrested by U.S. law enforcement for waging attacks against American interests would not necessarily be held by the Pentagon under several scenarios, including if foreign governments refuse to hand them over to U.S. military control.
Other exceptions would include if the person were a U.S. permanent legal resident or if transferring them to military custody would hurt the chances of obtaining a confession or cooperation from the terrorism suspect.
"A rigid, inflexible requirement to place suspected terrorists into military custody would undermine the national security interests of the United States, compromising our ability to collect intelligence and to incapacitate dangerous individuals," Obama said in the directive.
The White House said the rules Obama laid out on Tuesday made sure that an al Qaeda suspect "will be transferred from civilian to military custody only after a thorough evaluation of all of the relevant facts, based on the considered judgment of the president's senior national security team."
The Obama administration has long struggled over the best venue for prosecuting terrorism suspects, largely preferring criminal courts over military tribunals that Republicans and even some of the president's fellow Democrats have sought.
Tuesday's directive addresses concerns the White House had with the National Defense Authorization Act that Obama penned into law at the end of 2011.
The White House had raised concerns the bill could unduly broaden the armed forces' powers over suspected militants, requiring foreigners allied with al Qaeda to be held in military custody even if they were captured in the United States.
That would allow terrorism suspects to be kept in military custody indefinitely without trial. U.S. citizens were already exempted from the mandatory military detention requirement.
The final version of the bill that cleared Congress gave Obama the flexibility to waive certain provisions and to let him determine who would be held by the U.S. military.
The president's directive on Tuesday also gave the attorney general permission to make additional waivers on a case-by-case basis in consultation with other national security officials.
Other categories in which al Qaeda terrorism suspects would escape U.S. military custody under Obama's waivers include if it would hurt counterterrorism cooperation with another country. The directive would also waive military custody for individuals arrested in the United States on charges unrelated to terrorism and when the person was arrested by local or state authorities.
"The waiver authority and implementing procedures were specifically called for by those who spearheaded the legislation," said an Obama administration official. "Today's directive merely creates the implementing procedures required under the legislation."
(Editing by Cynthia Osterman)