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.
Brinkema, who did not immediately rule on the request, allowed the motion to be filed publicly because it did not reveal the issue involved. She has handled virtually all matters involving the case in closed session for several months.
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.
The problem for prosecutors is that pretrial decisions normally would not be appealed. The government, however, raised this appeal on national security grounds under a law governing use of classified information in a criminal trial.
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.
According to the New York Times, U.S. District Judge Leonie M. Brinkema ruled in secret last week that Moussaoui as a federal defendant has a constitutional right to some sort of pre-trial access to Ramzi Binalshibh. Judge Brinkema's ruling came as a surprise to no one and as a purely legal matter is a no-brainer. Of course, a capital defendant has a constitutional right to conduct discovery that might help provide him with a defense. To hold otherwise would be to deny such a defendant fundamental fair trial rights.
According to Cohen what is left as a good, old-fashioned standoff between two of the three branches of government. The courts are likely to continue to say to the government: you want to try Moussaoui in a capital case? Fine. You are going to obey the rules. And the government is likely to continue to say to the courts: we want to try Moussaoui without jeopardizing vital intelligence assets and we ought to be able to make that decision, your honor, not you. The only thing that makes this a breakable logjam is that Moussaoui's fate still is controlled by the executive branch.