WASHINGTON - For months, a national debate has raged over the fate of the 245 detainees at the United States military prison at Guantánamo Bay, Cuba.
But what may be an equally difficult problem now confronts the Obama administration in the 600 prisoners packed into a cavernous, makeshift prison on the American air base at Bagram in Afghanistan.
Military personnel who know Bagram and Guantánamo describe the Afghan site as tougher and more spartan. The prisoners have fewer privileges and virtually no access to lawyers. The Bush administration never allowed journalists or human rights advocates inside.
Problems have also developed with efforts to rehabilitate former jihadists, some of whom had been imprisoned at Guantánamo. Nine graduates of a Saudi program have been arrested for rejoining terrorist groups, Saudi officials said Monday.
President Obama must now decide whether and how to continue holding the men at Bagram, most of them suspected of being Taliban fighters. Under the laws of war, they are being held indefinitely and without charge. He must also determine whether to go forward with the construction of a $60 million prison complex at Bagram that, while offering better conditions for the detainees, would also signal a longer-term commitment to the American detention mission.
Mr. Obama tried last week to buy some time in addressing the challenges Bagram poses even as he ordered Guantánamo closed. By a separate executive order, Mr. Obama directed a task force led by the attorney general and the defense secretary to study the government's overall policy on detainees and to report to him in six months.
But human rights advocates and former government officials say that several factors - including expanding combat operations against the Taliban, the scheduled opening of the new prison at Bagram in the fall and a recent federal court order - will probably force the administration to deal with the vexing choices much sooner.
"How the Obama administration plans to deal with detention in Afghanistan is an open question," said Tina M. Foster, executive director of the International Justice Network, a human rights organization in New York. "How will this administration differ from the Bush administration in its conduct of detention in Afghanistan?"
The population at Bagram has increased nearly sixfold over the past four years, driven not just by the deepening conflict in Afghanistan but also by the fact that the Bush administration in September 2004 largely halted the movement of prisoners to Guantánamo, leaving Bagram as the preferred alternative to detain terrorism suspects.
Bush administration lawyers argued this month that the Bagram detainees were different from those at Guantánamo. Virtually all of the Bagram prisoners were captured on the battlefield and were being held in a war zone, the lawyers contended, and they could pose a security threat if released. On Thursday, Judge John D. Bates of the United States District Court for the District of Columbia gave the Obama administration until Feb. 20 to "refine" the government's legal position with respect to four men who are seeking to challenge their detention at Bagram under habeas corpus, a right that the Supreme Court has granted for detainees at Guantánamo.
The four plaintiffs were taken to Bagram from outside Afghanistan and have been imprisoned there without access to any legal process, many of them for over six years, said Ms. Foster, who is representing the detainees.
Judge Bates issued his order after Mr. Obama signed his directives on Thursday, and the judge cited the presidential orders as "indicating significant changes to the government's approach to the detention, and review of detention, of individuals currently held at Guantánamo Bay." He noted that "a different approach could impact the court's analysis of certain issues central to the resolution" of the Bagram cases as well.
At a White House briefing about the executive orders last Thursday, a senior administration official was asked whether terrorism suspects captured by American authorities would continue to be sent to Bagram. The official said not to expect any changes to existing policies in Afghanistan for at least six months, pending the completion of the task force's review.
A Justice Department spokesman, Dean Boyd, declined to comment on Judge Bates's order, saying that government lawyers were studying it.
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The challenges confronting the Obama administration at Bagram do not extend to the much larger American detention operations in Iraq, where the United States now holds about 15,000 prisoners. Under a security agreement with the Iraqi government, the United States will begin next month to release up to 1,500 detainees a month. Fighters captured and imprisoned in Iraq are afforded legal protections under the Geneva Conventions.
Human rights advocates are already pressing the administration to revamp the review process for releasing or transferring the Bagram detainees, all but about 30 of whom are Afghans. This process, which the military calls "unlawful enemy combatant review boards," involves reviews of the status of each prisoner every six months. Human rights lawyers criticize the process as a sham and have called for a return to the longstanding battlefield reviews called for by the Geneva Conventions.
More broadly, Mr. Obama's move away from the Bush administration's aggressive detention policies will have to be reconciled with his plans to increase combat operations in Afghanistan, a step that will almost inevitably generate new waves of detainees.
"The decisions about detention in and around Afghanistan are linked to strategic decisions Obama needs to make on the Afghanistan war," said Matthew Waxman, a professor at Columbia Law School who served in the Department of Defense overseeing detainee policies under the Bush administration. "Does a proposed ‘surge' in Afghanistan, for example, include an expanded detention mission? How does detention fit within a counterinsurgency strategy in Afghanistan?"
Mr. Waxman said one approach the Obama administration might consider is whether it can defend a narrower definition of enemy combatant than the broad one asserted by the Bush administration.
In 2005, the Bush administration began trying to scale back American involvement in detention operations in Afghanistan, mainly by transferring Bagram prisoners to an American-financed high-security prison outside of Kabul guarded by American-trained Afghan soldiers.
The American military has handed over about 20 to 30 detainees a month since 2007, or more than 500 detainees in all, according to Lt. Col. Mark Wright, a Defense Department spokesman.
But United States officials conceded more than a year ago that the new Afghan prison could not absorb all the Bagram prisoners. The officials have also acknowledged serious problems in the security-court system in Afghanistan in which the transferred detainees are being tried.
Another question confronting the Obama administration is whether to go ahead with the construction of a 40-acre detention complex to replace the existing prison. After the prison was created in early 2002, it became a primary screening site for prisoners captured in Afghanistan, Pakistan and elsewhere.
Harsh interrogation methods and sleep deprivation were used routinely, and two Afghan detainees died there in December 2002 after being beaten by American soldiers and hung by their arms from the ceiling of isolation cells.
Conditions and treatment have improved markedly since then, but there are still only minimal areas for the prisoners to exercise. The new detention center at Bagram is supposed to incorporate some of the lessons learned by the United States in Iraq. Classrooms will be built for vocational training and religious discussion, and there will be more space for recreation and family visits, officials said.
"The tragedy is, the U.S. is spending tens of millions of dollars building better detention facilities, but still has no process in place to handle these guys," said Sam Zarifi, director of Amnesty International's Asia-Pacific program, which is based in London.
Carlotta Gall contributed reporting from Kabul, Afghanistan.