WASHINGTON — The Bush administration assured the Supreme Court last December that Guantanamo Bay prisoners who felt they were unfairly being detained could have their cases thoroughly reviewed by a federal appeals court. Now, it’s not so clear.

When the first case arrived at the appeals court, the Justice Department told the judges they could look at the evidence but should act on the assumption that the military made the right decisions at Guantanamo Bay.

That assertion led to a testy exchange recently between an appellate judge, Merrick Garland, and a Justice Department attorney, Gregory Katsas. Judge Garland wanted an explanation for the contradiction. Mr. Katsas said there was no contradiction at all.

The exchange underscores the challenge facing the administration: It doesn’t want judges overseeing terrorism cases, but it can’t eliminate them from the process without first getting their approval.

Normally, a prisoner who believes he’s being unfairly detained can ask the courts to free him. It’s a right known as habeas corpus that dates back to the 1300s and was written into the Constitution.

But the administration says that right does not exist for Guantanamo detainees. For years, administration officials have tried to limit judges’ role in hearing detainees’ cases and twice the administration has been set back by the Supreme Court.

Currently, prisoners labeled enemy combatants can only challenge that finding in the U.S. Court of Appeals for the District of Columbia Circuit. The Supreme Court is considering whether that violates the principles of habeas corpus. A decision is expected by the end of June.

During arguments in December, Justice John Paul Stevens was particularly interested in what role the government envisioned for the appeals court. Was the court supposed to defer to the military? Or should the court conduct what’s known as a preponderance review, by balancing all the evidence and deciding whether the detainees really are enemy combatants?

Solicitor General Paul Clement was clear about what detainees could expect: “They’re specifically entitled to a preponderance review in the D.C. Circuit,” he told Justice Stevens.

Justice Stevens asked again. Mr. Clement again said the law called for a full review.

The outcome of the case means a great deal to detainees, who want an independent government branch to thoroughly review the military’s decisions.