The U.S. government, in an unusual retreat, urged a federal appeals court on Friday to set aside its ruling that allowed the United States to hold an American citizen as an enemy combatant without being charged.

In a filing to the U.S. Appeals Court in Richmond, Virginia, Justice Department lawyers said that since Jose Padilla — who was held by the U.S. military for more than three years as an enemy combatant — has been indicted by a civilian court in Florida, the case regarding his military custody was moot.

As a result, the government said the court should go ahead and set aside its September 9 ruling that allowed Padilla to be held by the military without charge.

That ruling had been seen as a significant victory and a legal precedent for the administration in its war on terrorism and its controversial policy of holding enemy combatants in prison for long periods without charges.

In the filing on Friday, the Justice Department lawyers also urged the court to approve the request to transfer Padilla to civilian custody so he can face trial in Florida. They said Padilla once lived in Florida and became involved with the other people named in his indictment there.

The appeals court had delayed Padilla’s transfer to civilian custody until the government explained why it used different facts to justify Padilla’s military detention from those included in last month’s indictment that charged Padilla with conspiracy to murder and aiding terrorists abroad.

The government’s filing said prosecutors had the right to limit charges in the indictment, particularly if that would allow them to avoid “sensitive evidentiary issues” that could implicate national security.

The appeals court also asked for the government’s and Padilla’s view on whether it should wipe out the September 9 ruling in light of the recent indictment.

The indictment did not refer to accusations against Padilla made by U.S. officials after his arrest in May 2002, that he plotted with al Qaeda to set off a radioactive “dirty bomb” in the United States. U.S. officials later said Padilla had plotted to blow up apartment buildings using natural gas.

Instead, the indictment only said Padilla and four other men had run a U.S. support cell providing money and recruits for a jihad campaign overseas.

“The fact that those charges involve different facts from those relied upon by the president in ordering petitioner’s military detention is not consequential,” the Justice Department lawyers wrote. “The president’s authority to detain enemy combatants during ongoing hostilities is wholly distinct from his ability to charge them for criminal conduct.”

Human rights activists and some lawmakers have questioned the government’s authority to detain Padilla without charges indefinitely as an “enemy combatant.”

Padilla’s lawyers have asked the U.S. Supreme Court to limit this authority. Attorney General Alberto Gonzales said the issue should be moot before the Supreme Court since Padilla has now been charged in civilian court.