His administration is facing a tighter deadline next week: transfer some detainees held at the prison or ask a military court for a third delay, a request the White House wants to avoid.
When Obama announced in January that he would close the prison within a year, about 10 cases already under review by the military commissions, including the one involving Khalid Sheikh Mohammed, the self-professed architect of the Sept. 11 terrorist attacks, were put on hold. The delay has to be renewed every 120 days, and the current deadline is Sept. 17. Six cases remain in limbo. Another delay would extend its total time to one year.
Senior Obama officials from the White House and Departments of Defense, State and Justice huddled at the end of last week and came up with at least three options to consider, sources told FOX News. They can ask for another delay, withdraw the charges without prejudice and transfer some of the cases to federal court where charges can be brought again, or maintain the status quo, which would include more pretrial hearings at Guantanamo next week.
Only 5 percent of the Gitmo detainees have been transferred since the president announced his intent to close the prison. In recent weeks, two detainees were sent to Portugal and another to his home in Afghanistan. About 220 remain.
It's an "extremely messy" situation, one official told FOX News.
Government lawyers in both the Obama and Bush administrations have said that an unspecified number of detainees should continue to be held without trial. Some of the evidence against them is classified or thin, and the government fears these most dangerous detainees could be released should they be given their day in court.
Both civilian federal jails and military prisons are being considered for potential future incarceration for prisoners facing criminal prosecution, military tribunals or long-term detention without a trial, government lawyers have said.
Obama officials are considering sending detainees to the Standish Maximum Correctional Facility in Michigan, which is scheduled to close this year because of state budget cuts. Some residents voiced their opposition to the plan at a town hall last month. Federal officials inspected the prison last month, but the White House says no decision has been made.
Congress has expressed strong concerns about the possibility of transferring some of the prisoners to the United States. Lawmakers blocked funding for transferring any detainees into the U.S. for the 2009 budget year ending Sept. 30.
FOX News' Catherine Herridge contributed to this report.