The decision is the court's latest rebuke to the way the George W. Bush administration defines the counterterrorism effort, and could force the administration to once again revise its procedures for handling captured Al-Qaeda and other terrorist suspects.
Bush, currently on a major European tour, expressed his disappointment during a news conference in Rome with Italian Prime Minister Silvio Berlusconi.
"We'll abide by the court's decision," Bush said. "That doesn't mean I have to agree with it. It was a deeply divided court and I strongly agree with those who dissented. And their dissent was based upon their serious concerns about U.S. national security."
For years, the administration has argued that the men being held at Guantanamo Bay are illegal enemy combatants without the rights that are usually accorded to prisoners of war.
Bush added: "We'll study this opinion and we'll do so with this in mind: to determine whether or not additional legislation might be appropriate so that we can truly say to the American people, 'We're doing everything we can to protect you.'"
One reason the administration has dubbed the detainees "illegal" combatants is that they were captured wearing no identifying uniforms and were otherwise not following the internationally accepted rules of war.
Yet at the same time, the administration has said that these captured fighters also are not normal civilians. The administration has therefore insisted that they don't have the rights of civilian prisoners to demand that prosecutors establish before a civilian judge that their incarceration is legal.
But in a five-to-four decision on June 12, the Supreme Court ruled against the administration. In the majority opinion, Justice Anthony Kennedy wrote that "the laws and constitution are designed to survive, and remain in force, in extraordinary times."
James Ross, the legal and policy director for Human Rights Watch (HRW), says the decision is important because it upholds the right of all detainees to challenge their detention. He said it also deals a major blow to the Bush administration's efforts to hold the suspects indefinitely without charges.
"The decision not only said that there was a common-law right under the U.S. Constitution for habeas corpus, but it said that the Detainee Treatment Act and the Military Commissions Act did not provide a suitable substitute for habeas corpus," Ross says. "So this was a government effort to really water down this fundamental right, and the Supreme Court just rejected that."
The U.S. Constitution guarantees that any detainee has a right to require that the authority that arrested him explain before a judge why he is being denied his freedom.
The four Supreme Court judges who opposed the majority decision criticized their colleagues for challenging what they called the administration's provisions for handling the prisoners. Chief Justice John Roberts called the operations at Guantanamo "the most generous set of procedural protections ever afforded aliens detained by this country as enemy combatants."
The ruling is the latest chapter in an already long story of the Supreme Court trying to define just how many legal rights and protections the foreign prisoners caught in the U.S. war on terror should have.
There are currently more than 250 men held in the U.S. facility at Guantanamo, down from a detainee population that at its height numbered some 600. The U.S. administration says it is holding the prisoners indefinitely -- that is, until the end of the war on terror -- and some have already been held more than six years.
U.S. authorities have not filed specific charges filed against most of those held at Guantanamo. However, there are plans to try some 80 of the detainees for war crimes, including roles in the September 11, 2001, attacks on the United States.
Rights From The Start
The Bush administration initially argued that the prisoners, because of their presumed illegal status as combatants, essentially had no rights whatsoever. Later it conceded that they had limited rights and set up a system to determine whether each detainee was in fact an illegal combatant and therefore subject to detention and trial.
However, the Supreme Court has now rejected that review system as inadequate to ensure their legal rights.
Specifically, the court overturned a lower-court ruling that had upheld legislation passed by Congress in 2006 that led to the U.S. administration setting up a review system. That 2006 law was controversial in part because it denied the right of a prisoner to bring his case before an individual judge.
The Supreme Court ruling represents the Bush administration's third setback over the legal status of the Guantanamo prisoners. On two previous occasions, the Supreme Court has ruled that the prisoners have a right to challenge their detention in civilian courts. But in both those cases, the administration persuaded Congress to pass laws sidestepping that requirement -- one being the Detainee Treatment Act and the other the Military Commissions Act. The administration was able to do so because, at the time, Congress was controlled by fellow Republicans.
Ross tells RFE/RL that he doubts the Bush administration will try again to have Congress pass another law that might answer the Supreme Court's objections. First, he says, both houses of Congress are now controlled by Democrats; and second, this is a general-election year in which most members are concerned with reelection campaigns.
Also, Ross says the administration may conclude that a further effort to do away with "habeas corpus" would be futile because the court ruled that the right of challenging detention goes deeper than statute law.
"This decision, I think, is particularly positive because it really does get to the root of the issue, finally," Ross says. "In earlier decisions, for example, the court said that under the federal law there were these protections. So [Bush and Congress] changed the federal law. But here they're saying, 'Look, it's deeper than that.' It is a decision that talks about the fundamental concept of habeas corpus under the constitution, not as a matter of simply federal law."
The facility at Guantanamo has proved to be one of the most controversial elements in the U.S.-led response to 9/11 and is widely criticized by human rights groups both inside and outside the country. Robert Gates, who succeeded Donald Rumsfeld as U.S. defense secretary, has said the facility should be shut down.
The Bush administration has defended its approach to the prisoners as necessary for conducting an efficient counterterrorism effort. It also says it has made extraordinary efforts to ensure that the prisoners are held in comfortable cells and that the men -- virtually all of them Muslims -- are allowed to practice Islam.
Charles Stimson, a senior legal fellow at the Heritage Foundation, a private policy research center in Washington, calls the ruling a setback. But he argues that it has positive ramifications for the U.S. government in its efforts against international terrorism.
Stimson tells RFE/RL that the ruling may ultimately lead to a civilian judge ruling that the vast majority of the detainees have been properly classified as enemy combatants. And he said he believes it indirectly upholds a major contention of the Bush administration since 9/11.
"By implication [it] states that the government can detain somebody as an enemy combatant for the duration of the hostilities," Stimson says. "So, once again, the administration has not been wrong in its initial, underlying assumption that, under the law of war -- Geneva Conventions -- people can be held for the duration."
Stimson said the ruling highlights what he called a "crucial need" for creating a durable legal framework for future captures of suspected enemies in what Bush calls the "war on terror."
"Clearly the legal framework that exists today was deficient, has been deemed deficient, and now there is a need for some action on behalf of the two branches of government that most need to weigh in on that, and that is the legislature and the executive branch," Stimson says.
Like Ross, Stimson says he, too, doubts the White House will make another effort to persuade Congress to pass legislation allowing detention without habeas corpus.