The Bush administration’s legal strategy in the war on terror is in serious disarray after the Supreme Court ruled, 5-3, that President Bush acted illegally when he established military commissions to try detainees suspected of war crimes.

The court’s sweeping decision yesterday also undermined, or rejected outright, a series of the administration’s legal arguments in a manner that could have ramifications far beyond the system for trying prisoners detained at Guantanamo Bay.

The new ruling came in a case brought by a Yemeni man, Salim Hamdan, who allegedly worked in Afghanistan as a driver and bodyguard for the founder of Al Qaeda, Osama bin Laden.

In a strikingly American scene, a Navy lawyer assigned to represent Mr. Hamdan stood in front of the Supreme Court building yesterday praising the justices for rejecting the actions of the commander in chief.

“It is a rebuke,” Lieutenant Commander Charles Swift told reporters. “It’s a return to our fundamental values and that return marks a high water point in American history. It means we can’t be scared out of who we are. And that’s victory, folks.”

Writing for the majority, Justice Stevens said the executive branch’s right to detain Mr. Hamdan was not in dispute, but imposing punishment on him is an altogether different proposition that requires greater safeguards.

“It bears emphasizing that Hamdan does not challenge, and we do not today address, the government’s power to detain him for the duration of active hostilities,” Justice Stevens wrote. “But in undertaking to try Hamdan and subject him to criminal punishment, the executive is bound to comply with the rule of law that prevails in this jurisdiction.”

Justice Stevens, writing for Justices Breyer, Ginsburg, Kennedy, and Souter, said the tribunals did not comply with the procedures Congress established for courts-martial under the Uniform Code of Military Justice. The majority was not persuaded by the administration’s arguments that the departure was justified by the threat of international terrorism. “Without for one moment underestimating that danger, it is not evident to use why it should require, in the case of Hamdan’s trial, any variance from the rules that govern courts-martial,” the majority concluded.

Justices Alito, Scalia, and Thomas each wrote dissenting opinions and joined in each other’s opinions, at least in part.

“We are not engaged in a traditional battle with a nation-state, but with a worldwide, hydra-headed enemy, who lurks in the shadows conspiring to reproduce the atrocities of September 11, 2001, and who has boasted of sending suicide bombers into civilian gatherings, has proudly distributed videotapes of beheadings of civilian workers, and has tortured and dismembered captured American soldiers,” Justice Thomas wrote. He warned that his colleagues “would sorely hamper the President’s ability to confront and defeat a new and deadly enemy.”

Speaking at a White House event about 90 minutes after the court’s decision was issued, Mr. Bush said he took the court’s view seriously, but he emphasized the danger of the Guantanamo prisoners.

“I’m not going to jeopardize the safety of the American people. People have got to understand that,” Mr. Bush said during a joint press availability with Prime Minister Koizumi of Japan. “I understand we’re in a war on terror, that these people were picked up off of a battlefield, and I will protect the people and, at the same time, conform with the findings of the Supreme Court.”

Mr. Bush also said he planned to pursue the court’s suggestion that Congress pass legislation authorizing and setting rules for the tribunals. “To the extent that there is latitude to work with the Congress to determine whether or not the military tribunals will be an avenue in which to give people their day in court, we will do so,” he said.

When pressed for more answers, the president protested that he had not had a chance to be briefed fully on the ruling.

“I’m sorry you had to waste your question,” Mr. Bush said brusquely to a Reuters reporter, Matt Spetalnick.

At a briefing later in the day, the White House press secretary, Tony Snow, sought to minimize the impact of the decision. “It doesn’t serve as a rebuke. What it says is that the Supreme Court disagrees with the method that has been designed right now by the administration, and it says, we want you to go back and consult with Congress,” Mr. Snow said. “Nobody gets a get-out-of-jail free card.”

However, legal analysts consulted by The New York Sun yesterday said the ruling was likely to have a far-reaching impact, because the justices went out of their way to poke holes in several legal arguments the administration has relied on to justify its tactics in a variety of areas.

“That really pulls the rug out from under the prosecution in a way that everyone ends up with egg on their faces,” a former judge advocate general of the Navy who joined an amicus brief supporting Mr. Hamdan, John Hutson, said.

“I think they ran roughshod over a number of cases,” a Berkeley law professor and former Justice Department lawyer, John Yoo, said.

The majority opinion concluded that a provision of the Geneva Conventions known as Common Article 3 applied to all prisoners captured in the war on terror, despite language limiting the provision to conflicts “not of an international character.” The high court said the fight with Al Qaeda was not international because the term should be interpreted literally, meaning between two or more nations.

“I’m flummoxed by it,” a law professor at Pepperdine University in California, Douglas Kmiec, said of the court’s finding. “I tend to think Al Qaeda cells being in Malaysia, the Philippines, London, Madrid, Washington, D.C., and Miami, is pretty international in scope.”

The Supreme Court used its conclusion to bolster Mr. Hamdan’s claim for a more ordinary trial, but the finding also has the consequence rejecting the Bush administration’s claim that the article’s prohibition on humiliating or degrading treatment does not apply to Al Qaeda prisoners.

“That is big,” Mr. Hutson, the dean of the Franklin Pierce Law Center in New Hampshire, said.

Asked if the ruling would cause a new review of aggressive interrogation procedures, Mr. Kmiec said, “Without doubt. As wrong as this opinion is, you can’t ignore it.”

The court rejected the Justice Department’s arguments that the authorization for the use of military force passed by Congress in September 2001 implicitly authorized tribunals such as those instituted by Mr. Bush. The repudiation was noteworthy because in 2004 the court upheld an expansive view of the use-of-force resolution as permitting the detention of an American captured on the battlefield.

The Bush administration has also used a broad reading of the 2001 resolution to justify the detention without trial or charge of Americans on American soil, as well as telephone and-email surveillance programs operated by the National Security Agency.

Mr. Yoo, who helped design the administration’s early legal strategy in the war on terror, called the court’s latest assessment of the use-of-force resolution “fairly cramped.”

“This decision is sort of inconsistent with Hamdi of two years ago,” he said.

Justice Kennedy declined to join in some aspects of Justice Stevens’s opinion, including a holding that the Geneva Conventions preclude a military tribunal from hearing testimony or seeing evidence to which the defendant is not privy.

Justice Thomas’s dissenting opinion rejected the majority’s application of the Geneva Conventions, arguing that enforcement the conventions, by their terms, is delegated “exclusively to the political branches.”

Justice Scalia, joined by Justices Thomas and Alito, filed an opinion forcefully asserting that the Supreme Court should not have ruled on the substance of the case because a law Congress passed in 2005, the Detainee Treatment Act, stripped the court of jurisdiction. Justice Scalia called Congress’s language “entirely clear,” but the court’s majority declared the dissent’s argument to be “counterfactual.”

While unwilling to adopt all of Justice Stevens’s reasoning, Justice Kennedy still seemed to chafe at the administration’s claims that the unusual threat posed by Al Qaeda merited some exceptions to traditional legal procedures. “The Constitution is best preserved by reliance on standards tested over time and insulated from the pressures of the moment,” he wrote.

Chief Justice Roberts did not take part in yesterday’s decision. Last year, while an appeals court judge, he heard arguments on Mr. Hamdan’s case and signed onto an opinion rejecting the challenge to the tribunal process. The Supreme Court’s ruling reversed that decision and, therefore, was something of a snub to the chief justice, who promised during his confirmation hearings to stay out of any case he ruled on at the appeals court.

Justice Breyer, in a concurring opinion joined by Justices Ginsburg, Kennedy and Souter, all but invited Mr. Bush to seek permission from Congress to establish a system of tribunals for the detainees. “Nothing prevents the President from returning to Congress to seek the authority he believes necessary,” Justice Breyer wrote. “Where, as here, no emergency prevents consultation with Congress, judicial insistence upon that consultation does not weaken our Nation’s ability to deal with danger.”

Mr. Yoo predicted that Congress would quickly reject the court’s language applying aspects of the Geneva Conventions to all war-on-terror prisoners held by America. “Congress is going to have to overrule that,” he said. “It’s going to waste a lot of time and energy that could be spent fighting the war on terrorism rather than having to respond to the Supreme Court for the second time.”