The Bush administration said it was housing and feeding the men well and allowing them access to religious material. But the U.S. denied them contact with the International Red Cross and their families.
The administration justified its policy by saying the captives didn't qualify for traditional protections of international law because they were illegal combatants -- among other things they did not wear uniforms on the battlefield.
Under worldwide pressure, however, Washington has begun releasing some of the prisoners deemed not to be a threat.
Now, according to "The Washington Post," at least 10 of those released have become involved in armed resistance in Afghanistan or Pakistan. Foreign Policy analyst James Phillips said this development can mean only one thing.
"That they're there [at Guantanamo] for a reason, and that they should stay there, many of them, and that the risks of releasing them are higher than people have generally appreciated before," Phillips said.
Phillips -- of the Heritage Foundation, a private policy-research center in Washington -- told RFE/RL the Defense Department should not have given in to international pressure.
Phillips said in a conventional war prisoners are held for the duration of the conflict. Because the "war on terrorism" is likely to be very long, he says he does not expect that the prisoners would be kept indefinitely. But to release any of them so soon, he said, was a mistake.
Phillips also disregarded the calls for an end to delays in the military hearings. He said that in wartime -- whether during a conventional war or the current conflict -- such proceedings are nearly impossible to conduct properly.
"The problem with trials [hearings] is you have to find witnesses in Afghanistan and fly them to wherever the trial's going to be held. And who can remember what happened three years ago?" Phillips said. "We may not be able to prove that before they were captured they were with Al-Qaeda or the Taliban, but releasing them because we can't prove they're members of those groups leads to the risk they'll go back and fight, and 10 of them have."
But the hearings are not the issue, according to James Ross, a senior legal adviser to the advocacy group Human Rights Watch. Speaking from his New York office, Ross told RFE/RL that in a conventional war, virtually all prisoners are merely held so they cannot fight, not because they are suspected of war crimes.
Ross said the same rules can apply to the men captured in Afghanistan. Even though they were fighting unconventionally, they merely need to be kept from rejoining the battle. But they also have the same rights as other war detainees.
"Anyone picked up doesn't necessarily require a trial, but they have to be held in accordance with the Geneva Convention," Ross said. "The U.S. has been holding these people, but not in accordance with any clear provisions of international humanitarian law. They're basically making up the rules in terms of who they can hold and for how long, rather than applying the Geneva Convention."
Ross said the Bush administration might only now be facing the problems of returning enemies to the battlefield -- not to mention the added embarrassment. But he said these problems have their roots in the very first days of the detentions, when U.S. officials should have begun acting within the law.
"Had the U.S., from the first, applied the system presented under international laws -- specifically the Geneva Conventions -- they would have avoided the difficult situation faced now," Ross said. "That would not have guaranteed that everyone released from U.S. custody wouldn't have become involved in the conflict there [in Afghanistan]. But at the same time, you also can't take steps to ensure that everyone in Afghanistan isn't going to pick up a weapon."
Ross said he does not know what the Bush administration should do at this stage about the prisoners at Guantanamo. He said so much of what the U.S. Defense Department has done the past three years has been wrong that it is hard to say what would now be right.