Mukasey, speaking at a Group of Eight meeting of justice and home affairs ministers in Tokyo, said he was disappointed with the decision because it would lead to "hundreds" of detention cases being referred to federal district court.
"I think it bears emphasis that the court's decision does not concern military commission trials, which will continue to proceed," he said. "Instead it addresses the procedures that the Congress and the president put in place to permit enemy combatants to challenge their detention."
The that foreign detainees held for years at Guantanamo have the right to appeal to U.S. civilian courts to challenge their indefinite imprisonment without charges.
President Bush said he strongly disagreed with the decision - the third time the court has repudiated him on the detainees - and suggested he might seek yet another law to keep terror suspects at the U.S. Navy prison camp.
Mukasey, who said he had not yet studied the decision, said the administration's next move had not been decided.
"Obviously we're going to comply with the decision," he said. "We're going to study both the decision itself, and whether any legislation or any other action may be appropriate."
Justice Anthony Kennedy, writing for the 5-4 high court majority on Thursday, acknowledged the terrorism threat facing the U.S. - the administration's justification for the detentions - but he declared: "The laws and Constitution are designed to survive, and remain in force, in extraordinary times."
In a blistering dissent, Justice Antonin Scalia said the decision "will make the war harder on us. It will almost certainly cause more Americans to be killed."
Sen. Lindsay Graham, R-S.C., called the ruling a "dangerous decision" because in the middle of a war, military officers could be dragged into federal court, reports CBS News correspondent Wyatt Andrews.
"Never in the history or warfare have we allowed enemy prisoners to go to a federal court and sue our own troops to be released," Graham told Andrews.
Kennedy said federal judges could ultimately order some detainees to be released, but he also said such orders would depend on security concerns and other circumstances. The ruling itself won't result in any immediate releases.
"The lesson here, and it's a costly one for the administration, is that it can't try the terror suspects through Guantanamo Bay without creating procedures that the Supreme Court signs off on," said CBS News chief legal analyst Andrew Cohen. ( .)