Several justices seemed deeply concerned that the government had gone too far in its plans to hold a special trial for Usama bin Laden's former driver on a conspiracy charge.
Some were downright indignant over the Bush administration's claim that a new federal law bars the high court from ruling in the case of Salim Ahmed Hamdan.
Hamdan's lawyer, Neal Katyal, said that the president "has the keys to the federal courthouse" under the law.
Without Chief Justice John Roberts, a conservative Bush nominated last year, the argument seemed lopsided against the government. Roberts voted in the case on a lower court and had to recuse himself. Justices Antonin Scalia and Samuel Alito hinted their support for the administration.
Justice Anthony M. Kennedy questioned Solicitor General Paul Clement about the legal safeguards for the trials. Justice Stephen Breyer also asked what would stop the president from holding the same type of trial in Toledo, Ohio, not just at the military prison in Guantanamo Bay, Cuba.
Hamdan claims the military commissions established by the Pentagon on Bush's orders are flawed because they violate basic military justice protections.
"This is a military commission that is literally unburdened by the laws, Constitution and treaties of the United States," Katyal told justices.
Scalia rebuffed a recusal request by five retired generals who support Hamdan's arguments. In a letter to the court, the generals had asked Scalia to withdraw from participating in the case because of remarks he made in a recent speech in Switzerland about "enemy combatants." Speaking at the University of Freiberg in Switzerland on March 8, Scalia said foreigners waging war against the United States have no rights under the Constitution.
Alito, the newest justice, suggested the court should wait until Hamdan's trial is over to allow him to question whether charging him with conspiracy violates the laws of war, as Katyal contends.
But Katyal brushed aside the contention. "The government has had four years to get their charges together on Mr. Hamdan," he said.
Hamdan, a Yemeni who was captured in Afghanistan in November 2001, is charged with conspiracy to commit war crimes, murder and terrorism. He claims he is an innocent father of two young daughters and worked as a driver for bin Laden in Afghanistan only to eke out a living for his family.
The Bush administration says he is a trained terrorist who should be tried for war crimes before a special military commission, the first such trial since the aftermath of World War II.
Roberts left the bench before arguments began and won't be involved in the decision.
Hamdan is among about 490 foreigners being held as "enemy combatants" at the military prison in Guantanamo Bay. Ten of the men, including Hamdan, have been charged with crimes.
Justices ruled two years ago that the government could detain enemy combatants but not shut off their access to U.S. courts.
In this follow-up case, justices are considering the government's plans for trials before a panel of military officers.
Hamdan's trial was halted last fall when a federal judge ruled that he could not be tried by a U.S. military commission unless a "competent tribunal" determined first that he was not a prisoner of war under the 1949 Geneva Convention.
Roberts was on a three-judge panel of the U.S. Court of Appeals for the District of Columbia Circuit that said the trial could resume, and Hamdan's attorneys appealed to the Supreme Court.
The court could dodge a major ruling in the case, on grounds that the new law stripped the justices' authority to consider it. The law passed late last year bars Guantanamo prisoners from filing petitions to fight their detentions, and the administration claims this law retroactively voided hundreds of lawsuits.
The case is Hamdan v. Rumsfeld, 05-184.