A quick setback for Padilla.

The Supreme Court agreed today to let the government transfer Jose Padilla to from a military to civilian custody.

The United States Court of Appeals for the Fourth Circuit, in Richmond, Va., refused last month to allow Mr. Padilla to be transferred to civilian custody, declaring that the Bush administration gave the appearance of pushing for the transfer to prevent the Supreme Court from hearing the case and ruling on the government's ability to hold an American citizen like Mr. Padilla outside the civilian criminal justice system. The Justice Department assailed the ruling as an "unwarranted attack" on presidential discretion.

The clash between the Fourth Circuit and the administration was remarkable, since the circuit is regarded as perhaps the most conservative of the federal appellate courts and therefore generally an ally of the Bush White House. Indeed, in September, the Fourth Circuit affirmed President Bush's power to hold Mr. Padilla as an enemy combatant.

The Fourth Circuit's stance was surprisingly harsh, calling the administration on what it perceived as manipulation of the judicial system. Apparently, the Supreme Court did not buy that characterization.

UPDATE: Linda Greenhouse provides a more detailed report:

The United States Court of Appeals for the Fourth Circuit... issued an opinion on Dec. 21 that suggested in stinging terms that the administration was now manipulating the federal court system, with "intentional mooting," in order to avoid Supreme Court review of the case.

In his opinion for the appeals court, Judge J. Michael Luttig said that while there might be valid reasons for the administration's request for an "eleventh-hour transfer" of Mr. Padilla, "any legitimate reasons are not evident, and the government has not offered explanation." He continued: "On an issue of such surpassing importance, we believe that the rule of law is best served by maintaining on appeal the status quo in all respects and allowing Supreme Court consideration of the case in the ordinary course."

Judge Luttig, the author of the Fourth Circuit decision that Mr. Padilla has appealed to the Supreme Court, has generally been supportive of the administration's claims of broad executive authority and was on the short list for the court's recent vacancies. His opinion this time set off a flurry of new Supreme Court filings, led by the administration, which a week ago asked the justices to "recognize the release and transfer of Jose Padilla" from the Charleston brig to the federal prison in Miami.

Solicitor General Paul D. Clement told the court that the Fourth Circuit's order refusing the transfer "is based on a mischaracterization of events and an unwarranted attack on the exercise of executive discretion, and, if given effect, would raise profound separation-of-powers concerns."

In response, Mr. Padilla's lawyers told the court on Friday that while their client was "certainly eager to be released from the military brig where he has been held virtually incommunicado and in solitary confinement for the past three and a half years," the justices should wait the two weeks that it would take to consider his underlying appeal "in an orderly fashion."

The lawyers said "it would be highly imprudent for this court to hold that the government has an unlimited ability to transfer prisoners in military custody while their habeas petitions are pending." Mr. Padilla's Supreme Court appeal, Padilla v. Hanft, No. 05-533, began as a petition for a writ of habeas corpus, a challenge to the constitutionality of his confinement.

On Tuesday, the administration filed another brief with the court, reiterating the request for a transfer while conceding that Mr. Padilla's case would still be eligible for Supreme Court review even if he were no longer in military custody. "Granting the application will not prejudice this court's consideration of Padilla's petition," the brief said, adding, "It would, however, eliminate the anomaly of a citizen being held by the military against the wishes of both the executive and the detainee (at least in all but the short run)."

With the Supreme Court still technically on its Christmas recess, its action late Wednesday afternoon came as something of a surprise. "The government's application presented to the chief justice and by him referred to the court is granted," the order said.

I note that there is room to say that the Supreme Court didn't really so much disagree with the 4th Circuit as respond to Clement's assurance that the case would not be moot, even if Padilla were transferred. But the 4th Circuit knew that too. The government can't on its own volition manipulate the facts into mootness. The "voluntary cessation doctrine" prevents mootness, whether the government points that out or not. Luttig stressed the government's failure to give reasons for changing its approach to dealing with Padilla, and, facing the Supreme Court, the government relied on the executive's discretion in such matters and the Supreme Court seems to have accepted that.