But the detainees point out that they don't have lawyers in the military hearings and instead are assigned "personal representatives" by the government. That appeared to trouble both Justices Stevens and Souter.
"Is that personal representative also under an obligation to report back to the military anything that might be unfavorable to the person he is supposedly representing?" Souter asked.
In the months after the Sept. 11 attacks, the administration quickly decided to send detainees to Guantanamo, believing that if the detainees were held off of U.S. soil they would not get access to U.S. courts.
Congress mandated that detainees receive hearings called Combatant Status Review Tribunals to determine whether they should be released or named as enemy combatants. Of the some 800 people sent to Guantanamo, roughly 500 have been released.
Human rights groups around the world have criticized Guantanamo -- and Attorney General Michael Mukasey said in his confirmation hearings that the detention center has given the United States a "black eye." But military lawyers say they are proud of the current system and believe it provides a fair system for review.
Brigadier Gen. Cameron A. Crawford, the deputy commander of Joint Task Force Guantanamo, told ABC News, "I believe that 40, 50 years from now when our children and grandchildren are studying Guantanamo, I believe that history will have judged that we did the right thing at the right time, in face of overwhelming criticism both domestically and most certainly on an international basis."
Military lawyers say that the system at Guantanamo is necessary because the federal court system in America is simply not well suited to handle the legal issues that arise in a war with an enemy like al Qaeda. The government also has created a system of military commissions to try suspected terrorists at Guantanamo.
Capt. Pat McCarthy, the U.S. government's lead counsel in Guantanamo, describes scenarios of capture that have complicated the government's attempt to gather evidence.
"We had to grab as much stuff as we could grab in the house and get out the door with it before the house was inundated with cohorts of the individual that we are taking custody over," he said.
Any chance to gather evidence was rushed, McCarthy said. "So what you have is large green trash bags full of computers, full of weapons, full of letters, you have all of that sort of thing."
He said that such evidence would never be accepted in a federal court. "I can assure you that if you attempt to take that sort of evidence into federal district court you will not be able to convict, period."
But others disagree.
Michael Greenberger, law professor at the University of Maryland School of Law, said the U.S. courts would be able to handle the detainees if the administration lost the case.
"The detainees will have to be brought back to the United States and held either as enemy combatants or prisoners of war here," Greenberger said. "That is not an unusual situation. During World War II both enemy combatants and prisoners of war were held in the United States."
Greenberger said he believes that a loss for the government would cause Guantanamo to eventually close. If detainees got into federal courts, that would undercut the administration's main reason for sending them there in the first place -- it believed they would not have access to courts because they weren't on U.S. soil.