US District Judge Leonie Brinkema said on Monday that it was "very difficult for this case to go forward" after prosecutors revealed that a lawyer for the Transportation Security Administration had violated her order of barring witnesses from any exposure to trial testimony.
Brinkema sent the jury home until Wednesday while she considers her options.
If she bars the government from pursuing the death penalty, the trial would be over and Moussaoui would automatically be sentenced to life in prison without the possibility of release. The government would probably appeal that ruling.
A hearing is scheduled for Tuesday to determine the scope of the problem. The TSA lawyer, Carla Martin, and most of the seven witnesses - past or present employees of the Federal Aviation Administration who received emails from Martin - are expected to testify.
The judge said she had "never seen such an egregious violation of a rule on witnesses", and prosecutor David Novak agreed that Martin's actions were "horrendously wrong".
Defence lawyer Edward MacMahon asked Brinkema to dismiss the government's death-penalty case, saying, "This is not going to be a fair trial."
At the very least, he said the government's FAA witnesses should be excluded. But prosecutor Novak protested that they represented "half the government's case".
"There is no way to un-ring the bell," the defence said in a court filing on Monday night. "The FAA witnesses have been tainted and no matter how much they contend that they can be truthful, they have been coached concerning the defects in the government's case and how to overcome those defects."
Moussaoui is the only person
charged in the US for 9/11 attacks
In its filing, the government said there was no need to exclude the FAA witnesses from testifying, saying the violation of the court's order, "while egregious", could be remedied when the witnesses were questioned in front of the jury.
Martin's emails to the upcoming witnesses included excerpts of the government's opening statement and Martin's assessment that the opening statement "has created a credibility gap that the defence can drive a truck through".
She expressed concern that FAA witnesses would be made to look foolish on cross-examination and warned them to be prepared for certain topics.
Brinkema said the violation was compounded by the fact that Martin emailed the witnesses jointly, violating standard practice against joint interviews of witnesses.
"What that leads to is the very real potential that witnesses are rehearsed, coached or otherwise that the truth-seeking concept of a proceeding is significantly eroded," Brinkema said.
Efforts to reach Martin for comment by telephone were unsuccessful.
Brinkema said she would also reconsider the defence's request of last week for a mistrial - made after a question from Novak suggested to the jury that Moussaoui might have had an obligation to confess his terrorist connections to the FBI even after he had invoked his right to a lawyer.
Of the seven witnesses whose testimony was potentially tainted, three were expected to be government witnesses and four were expected to be defence witnesses.
Moussaoui appeared amused as the lawyers debated how to proceed. Leaving the courtroom, he said, "The show must go on".
Moussaoui pleaded guilty in April to conspiring with al-Qaida to hijack aircraft and commit other crimes, and the current trial will determine his punishment: life in prison, or death.
He is the only person charged in the US with the 11 September 2001 attacks, but he has specifically denied any links to 9/11 and says he was training to be part of a possible future attack. Prosecutors, to obtain the death penalty, must prove that Moussaoui's actions resulted in at least one death on September 11.