Judge Leonie Brinkema has adjourned the hearing for 48 hours to consider a defence motion to strike out the option of execution after a government lawyer broke rules on coaching witnesses.
Prosecutors have called for Moussaoui, who has already admitted to conspiring to fly a hijacked airliner into the White House, to face the death penalty. The defence wants a term of life imprisonment.
Judge Brinkema scheduled an evidence hearing in her Virginia courtroom on Tuesday to assess the extent to which seven witnesses had been tainted.
"It is very difficult for this case to go forward," said Judge Brinkema. "In all the years I have been on the bench I have never seen such an egregious violation of the court's rules on witnesses".
"This is the second significant error by the government affecting the constitutional rights of this defendant. More importantly it affects the integrity of the criminal justice system of the United States," she said.
Trial fairness questioned
Judge Brinkema said contrary to her previous instructions, a lawyer identified only as a woman called "Martins" from the Transportation Security Administration, spoke in detail to federal aviation officials due to testify in the case.
"Martins" had even arranged for witnesses to see a transcript of the trial’s opening statements last week.
Immediately the defence filed a motion for the dismissal of the death penalty case against Moussaoui.
"The proceedings should really be dismissed and Mr. Moussaoui sentenced to life in prison," said defence attorney Edward MacMahon. "We are not going to get a fair trial."
Prosecutors said any concerns about the integrity of the case could be corrected by a vigorous defence cross-examination of the witnesses concerned.
"We are really not in a position to defend her ["Martins" conduct. The question is where do we go from here?" said prosecution lawyer David Novak.
Mr MacMahon argued to strike all of those affected from the case, as four of the witnesses in question were supposed to testify for the defence.
Mr MacMahon said he did not see how he could cross-examine his own witnesses.
Moussaoui defiant
Government prosecutors allege Moussaoui lied to investigators in 2001 allowing the September 11 attacks to go ahead, and so shares guilt in nearly 3,000 deaths.
As he was led out of the courtroom on Monday, Moussaoui shouted "the show must go on".
Moussaoui has largely obeyed Judge Brinkema's instructions to remain silent throughout the trial after a string of outbursts during initial jury selection hearings last month.
But every day, he has lobbed a final comment to the public galleries after the jury left court, usually a variation on "Allah Akbar. God Curse the United States."