The U.S. government asked a judge last week to halt all proceedings in the case of accused Sept. 11 conspirator until certain issues are resolved by an appeals court.
A government official, who would not be identified by name, indicated one of the issues is whether Moussaoui, a French citizen, should have the right to question Ramzi Binalshibh, who the indictment says was an al Qaeda operative in contact with Moussaoui.
The government is appealing an order by U.S. District Judge Leonie Brinkema in the Binalshibh matter.
The Justice Department has said it wants to keep the case in the criminal justice system, but Brinkema's ruling could force the administration to move the case to a military tribunal.
The administration has been worried about giving Moussaoui access to Binalshibh, because it doesn't want him revealing certain information in a public trial.
"Under the current circumstances of this case, it would be impracticable to continue this litigation until the issues presented to the 4th Circuit are resolved," said the motion by U.S. Attorney Paul McNulty.
Moussaoui is the only person charged in the United States as a conspirator with the Sept. 11, 2001 attackers who flew planes into the World Trade Center towers and the Pentagon. The Justice Department is seeking the death penalty for him.
Moussaoui has acknowledged he belongs to al Qaeda but has denied participation in the Sept. 11 attacks.
Authorities believe Binalshibh, who was captured in Pakistan last October, was a key figure n the Hamburg, Germany cell that carried out the suicide attacks.
The government has been worried that he could reveal information about al Qaeda that the administration doesn't want to be made public.
Moussaoui, who is representing himself, has asked for access to Binalshibh. In a criminal trial, a defendant would normally be able to question a witness whose testimony could exonerate him.
U.S. v. Moussaoui already has a tortuous past, says CBS News Legal Analyst Andrew Cohen. But the latest legal conundrum it has generated is by far the most significant. It might prompt the Bush administration to give up on prosecuting the man who wanted to learn to fly planes without learning how to take off or land. And it might force the government to radically alter the way it handles terror suspects.