McCrystal said last week that the prison would be handed over to the Afghans in January. It is unlikely the U.S. would send terrorism suspects to Bagram once it is under the control of the Afghan government. As a result, some officials in Washington want to slow down the hand-over, at least until other options are examined.
The Obama administration is hoping to buy a state prison in Thomson, Ill., to turn it into a federal facility to house some terrorism suspects. But the administration has indicated that any such suspects held at the prison would be limited to detainees facing prosecution and those currently at Guantanamo.
Thomson is not viewed as an option for suspected terrorists captured outside the U.S. because of near-certain resistance from Congress and the public. "Thomson is there to clean up a mistake, not to serve as a permanent model for future detentions," said Tom Malinowski, the Washington advocacy director of Human Rights Watch.
In addition, any suspected terrorist held inside the U.S. would probably have the right to challenge his detention in federal courts. Bagram, for now, is outside the reach of U.S. courts.
In April 2009, U.S. District Judge John D. Bates ruled that detainees captured outside Afghanistan and shipped to Bagram could seek court review of their detention, like prisoners at Guantanamo Bay. Bates' ruling allowed the detainees to file habeas corpus petitions seeking their freedom.
Bates put his ruling on hold after the administration filed an appeal, to the chagrin of human rights groups who said it conflicted with Obama's pledge to overhaul George W. Bush-era detention policies. If the original ruling is upheld, it would undermine a key legal justification for using Bagram.
Another uncertainty, officials said, is that it's not known whether Afghan President Hamid Karzai would continue to accept having non-Afghan prisoners at Bagram.
The prison that opened this year replaced the Soviet-era hangar that had been used since 2002 to house prisoners, sometimes under harsh conditions.
An official familiar with discussions over Bagram said McCrystal supports using the prison for militants picked up in Pakistan who have a "direct impact on the fight in Afghanistan." That would include Mullah Abdul Ghani Baradar, the Taliban leader captured in Pakistan in February, the official said.
Baradar's capture renewed a debate over where to put high-level detainees. But as an Afghan Taliban leader captured in Pakistan, Baradar does not pose as many legal and political complications for U.S. officials as extremists seized in Yemen, Somalia or elsewhere.
When the issue came up at a Senate hearing last week, officials ducked the question. Navy Adm. Eric T. Olson, head of U.S. Special Operations Command, was asked where the U.S. would send a suspect captured in Yemen.
"That's a question that, on so many levels, we would have to go into closed session" to answer, Olson replied.