The Justice Department on Wednesday acknowledged that U.S. District Judge Leonie Brinkema could respond by dismissing the case, but asked her to postpone any punishment pending an appeal.
Moussaoui is the only person charged in the United States as a conspirator in the Sept. 11, 2001, terrorist attacks. If his case is dismissed, the government has said it has the option of sending the French citizen's case to a military tribunal.
In court papers and past hearings, Moussaoui has pledged his loyalty to Osama bin Laden but denied involvement in planning the Sept. 11 airplane hijackings in which more than 3,000 people died.
Allowing him to question terrorist colleagues "would needlessly jeopardize national security at a time of war with an enemy who has already murdered thousands of our citizens," the government said in a written notification to the court of its position.
"Consequently, the government cannot, consistent with the interest of national security, comply with the court's order" of Aug. 29.
The order granted Moussaoui's request to question Khalid Shaikh Mohammed, who is considered the mastermind of the Sept. 11 attacks, and Mustafa Ahmed al-Hawsawi, a suspected paymaster for al Qaeda.
In January, Brinkema granted a similar request by Moussaoui to question an al Qaeda planner of Sept. 11, Ramzi Binalshibh. The government also refused to make him available.
The government said it was "exercising its right not to disclose classified information" that could be revealed by the al Qaeda prisoners.
Brinkema's other options include exclusion of government evidence, barring the death penalty and dismissing some counts in the case.
The dispute between the Bush administration and the judge has delayed a trial for Moussaoui. Prosecutors previously warned of grave consequences if Moussaoui was allowed to interrupt interrogations of prisoners who may be providing information on terrorism operations.
Brinkema concluded in the January and August rulings that Moussaoui's constitutional right to potentially favorable witnesses outweighs the national security concerns. She ordered use of satellite communications to connect Moussaoui with the prisoners, who are being held in undisclosed locations.
A panel of the 4th U.S. Circuit Court of Appeals, which has heard oral arguments on Moussaoui's request for access to Binalshibh, previously said it was ready to decide that case. But the appellate judges deferred, saying the government first must disobey the order — as it had done — and find out what sanctions Brinkema will impose.
The Sixth Amendment to the Constitution normally grants defendants the right to compel the appearance of potentially favorable witnesses for pretrial questioning and to testify at trial. The government argued the amendment doesn't apply to wartime captives held outside the United States.
Brinkema had concluded that Moussaoui, who is representing himself, and a team of court-appointed lawyers assisting him had convinced the court the prisoners had made statements that would support Moussaoui's denial of involvement in the Sept. 11 conspiracy.
Moussaoui, who was arrested in Minnesota a month before the attacks, is charged with participating in a broad conspiracy that including planning for the Sept. 11 attacks, as well as other aspects of a terrorist fight against the United States: religious edicts to kill U.S. soldiers in Somalia, training of al Qaeda terrorists for a holy war and attempts by al Qaeda to obtain components of nuclear weapons.
Even if the al Qaeda witnesses did not prevent a guilty verdict, they could influence the second phase of a trial, where jurors would determine whether Moussaoui receives the death penalty.
Civil liberties advocates have criticized the Bush administration for putting several terrorist cases beyond the reach of the civilian justice system, and they are worried that the same will occur in the Moussaoui case.
The federal government has already declared two citizens and a third man "enemy combatants," an innovative legal designation that, the government asserts and courts have agreed, allows the indefinite detention of a person without charges being filed.
Among the 600 men imprisoned at Guantanamo Bay, Cuba, President Bush has designated six for military tribunals, which will be secretive, have strictly limited appeals and be conducted under looser rules of evidence than civilian courts.
The other prisoners there are classified as unlawful combatants, and are treated neither as criminal defendants nor prisoners of war.