The military imprisoned Jose Padilla without charges or a trial for more than three years, accusing him of plotting to detonate a radiological "dirty bomb" and conspiring to blow up apartment buildings in the United States.
Last week, a federal grand jury indicted Padilla on terrorism charges without mentioning the bombing plots.
Yesterday, a federal appeals court ordered the government to explain why.
The Richmond-based U.S. Court of Appeals for the 4th Circuit declined to authorize Padilla's transfer from military to Justice Department custody until the government elaborates on "the different facts that were alleged by the President to warrant Padilla's military detention" as compared with "the alleged facts on which Padilla has now been indicted."
In a brief order, the court indicated that it could seek to block the transfer entirely if a three-judge panel is not satisfied with the government's answers.
The court also said it might vacate its earlier decision that affirmed the president's power to detain Padilla as an "enemy combatant" in the first place, which would be a blow to the Bush administration as it continues looking for terrorists.
Padilla, a former gang member who has been at the center of a fierce political and legal struggle over governmental powers since the Sept. 11, 2001, terror attacks, was arrested in Chicago in 2002 and declared a combatant by President Bush a month later. Padilla has been held in a U.S. naval brig since.
Legal experts said it was hard to assess the significance of yesterday's order because much remains uncertain. If the 4th Circuit blocks Padilla's transfer to the Justice Department, that could set up a showdown between the executive and judicial branches.
The court also could take the rare step of withdrawing the opinion from September that backed the president's power to indefinitely detain Padilla -- a U.S. citizen captured in the United States -- without any criminal charges. That would deprive the government of a legal precedent it has hailed as vital to fighting terrorism.
At the very least, said Carl Tobias, a law professor at the University of Richmond, "the judges seem to be concerned about the government's change of position and want some explanation. You can see a suggestion of discomfort, or some unhappiness with the government."
Bryan Sierra, a Justice Department spokesman, said the department "intends to comply fully with the 4th Circuit's order" and would not comment further.
Jonathan Freiman, an attorney for Padilla, said he was "disappointed that Mr. Padilla's transfer to the civilian justice system has been delayed. We've been asking for 31/2 years for him to be charged with a crime and tried before a jury of his peers. We think that's the birthright of every American citizen."
Under yesterday's order, Padilla's transfer to the federal prison in Miami, where he was indicted, would be delayed until at least Dec. 16. That's the date the 4th Circuit set to receive defense briefs on whether its earlier ruling should be vacated. Government briefs are due Dec. 9.
The three-page order was entered at the direction of Judge J. Michael Luttig, with the concurrence of Judges M. Blane Michael and William B. Traxler Jr. The same three-judge panel issued September's ruling.
Padilla, a Muslim convert, was arrested at Chicago's O'Hare International Airport in May 2002. He was sent to a naval brig in South Carolina after being designated an enemy combatant.
The government initially alleged that he was plotting a radiological attack. Justice Department officials then outlined separate allegations in 2004, that Padilla had plotted with high-ranking al Qaeda operatives to blow up U.S. apartment buildings using natural gas.
Attorneys for Padilla, joined by a host of civil liberties organizations, blasted the detention as illegal and said they feared that the military would be allowed to hold anyone.
In its September ruling, the 4th Circuit panel accepted the government's argument that Bush not only had the authority to detain Padilla but that such power is essential to preventing terrorist strikes.
Padilla is one of two U.S. citizens held as enemy combatants since the terrorist attacks on the World Trade Center and Pentagon. The other, Yaser Esam Hamdi, was released and flown to Saudi Arabia last year after the Supreme Court upheld the government's power to detain him but said he could challenge that detention in U.S. courts.
The indictment unsealed last week in federal court in Miami charged Padilla with being part of a violent terrorism conspiracy rooted in North America but directed at sending money and recruits overseas to "murder, kidnap and maim."
It did not mention the dirty bomb, apartment building allegations or any plot to attack inside the U.S.