US District Judge Leonie Brinkema said the case could continue but dealt a stinging rebuke to the government.
"I don't think in the annals of criminal law there has ever been a case with as many significant problems," she told the court.
Judge Brinkema's ruling came after a controversy over apparent witness coaching by a government lawyer that the defence said prejudiced Moussaoui's chances of a fair trial.
She struck out all testimony from witnesses having to do with aviation issues, which the prosecution had said made up half of its case against Moussaoui.
Judge Brinkema later postponed the hearing to allow prosecutors time to decide whether to appeal her ruling.
She had earlier held a hearing without the jury, to assess the damage done to Moussaoui's chances of a fair trial by Carla Martin, a lawyer for the Transportation Security Administration.
The episode threatened to derail what could be the US government's only chance to secure a death penalty in connection with the September 11 attacks in 2001, which killed nearly 3,000 people.
Martin coached
Defence lawyers said Ms Martin's apparent attempt to coach witnesses means Moussaoui, a Frenchman of Moroccan descent, could never have a fair trial.
Judge Brinkema had already said the integrity of the US criminal justice system was on the line.
Prosecutors said that throwing out the trial would be too "draconian" and that the possible contamination of witnesses can be corrected under cross-examination.
Ms Martin, who arrived at the Virginia courthouse pursued by television cameras, refused to testify, as is her right, saying she had so far been unable to retain a lawyer.
Judge Brinkema warned her she could be subject to criminal or civil contempt of court proceedings, and ordered her to get a lawyer so she can appear later Tuesday or at the latest by 8:30 am (1330 GMT) Wednesday.
Four witnesses so far questioned said Ms Martin's interventions, via a flurry of emails, telephone calls and in person, had not convinced them to change their testimony.
But they conceded they had seen transcripts of the trial's opening statement and in some cases discussed it with her.
They said they were unaware of Judge Brinkema's instructions that they should not see or discuss any such material.
Lynne Osmus, head of intelligence at the Federal Aviation Administration (FAA), said Ms Martin's comments in an email about the trial's opening statements last week did not make much sense to her and would not sway her testimony.
Telephone calls
Claudio Manno, deputy assistant administrator for security and hazardous materials at the FAA, took a similar line.
He also admitted that he had been included on a telephone call with another person and prosecutor David Novak, as part of preparing witness testimony, in what could also be interpreted as an infringement of Judge Brinkema's instructions.
Mr Novak said that the conversation was simply about logistics and included no substantive discussion about the case.
Moussaoui watched the proceedings in silence but as he was led from court for a lunchbreak, he shouted "God Curse America, nation of Shit."
In court papers the defence argued the witnesses, all of whom are or were employed by the FAA, had been irreversibly tainted and so the trial should be dismissed.
The defence urged the judge to dismiss three of the seven witnesses, who represent a crucial part of the prosecution case but prosecutors argued that throwing out the case would be too harsh.
Moussaoui admitted last year to having conspired to fly a hijacked airliner into the White House, in what he said was a planned follow-up to the September 11 strikes which killed nearly 3,000 people.
Although he was in jail at the time of the attacks, prosecutors argue
Moussaoui should be executed because he knew Osama bin Laden's group planned to use airliners as weapons but did not tell US authorities.