The government said on Monday that it would not allow Zacarias Moussaoui to question a captured al Qaeda member - a move it acknowledged could result in the dismissal of the case.
Federal prosecutors said US national security would be damaged as a result of a District Court's order allowing Moussaoui, the only person charged in connection with the 11 September attacks, to question Ramzi bin al-Shibh.
Protecting national security
"The deposition, which would involve an admitted and unrepentant terrorist (the defendant) questioning one of his al Qaeda confederates would necessarily result in the unauthorized disclosure of classified information," the government said in a deposition in which it refused access to bin al-Shibh.
"Such a scenario is unacceptable to the government, which not only carries the responsibility of prosecuting the defendant, but also of protecting this nation's security at a time of war with an enemy who has already murdered thousands of our citizens," it said.
US District Judge Leonie Brinkema now has the option of dismissing the indictment or imposing some other sanction on the government.
But the case would not necessarily be over even if she dismisses the indictment because the government could still appeal to the Court of Appeals and to the Supreme Court.
It also has the option of trying Moussaoui in a military tribunal which would give him fewer protections.
bin al-Shibh: Key witness
Brinkema ruled in January that Moussaoui and his lawyers could question bin al-Shibh via videoconferencing. Her order sparked a flurry of appeals and led Brinkema to indefinitely postpone the trial.
The government says Moussaoui, who has admitted to being a member of al Qaeda, has no right to question bin al-Shibh who was captured last year in Pakistan and is being interrogated in a secret location.
But Moussaoui's court-appointed lawyers say he has a constitutional right to question anyone who can help prove his innocence.
And Moussaoui, who is acting as his own attorney, says bin al-Shibh can prove his innocence.
A Frenchman of Moroccan descent, Moussaoui, who was arrested shortly before the 11 September attacks on immigration charges, faces the death penalty if convicted.
The US accuses him of being the "20th hijacker," who was to join the 19 others that crashed jetliners into New York City's World Trade Towers, the Pentagon and a field in Pennsylvania, killing 3,000.