Leonie Brinkema, a US district judge, said the prosecution could call "untainted" aviation witnesses and produce "untainted physical evidence".
"I'm fully aware of how important it is for this matter to become resolved one way or the other," Brinkema told lawyers from each side before issuing her order.
"I agree that it would be unfortunate if this case could not go forward to some final resolution."
Earlier this week, Brinkema barred some witnesses from testifying because they had been improperly contacted by a government lawyer, Carla Martin.
Prosecutors had asked Brinkema to reconsider her decision in the government's only case involving the hijackings that killed about 3000 people when she threw out the aviation component.
Prosecutors said much of the aviation testimony was undisputed and they could find witnesses with whom Martin did not discuss trial proceedings.
The aviation testimony affects about half the government's case against Moussaoui.
Moussaoui, an al-Qaida member who has pleaded guilty to conspiracy in the 11 September attacks, is on trial to see if he will be executed or get life in prison.
Moussaoui says he was not
involved in the 9/11 attacks
The aviation testimony was expected to deal with how much information the Federal Aviation Administration had about possible threats to airlines and also discuss pre-11 September security measures.
In a court filing on Thursday, Moussaoui's lawyers said it would be difficult to find any witness who had not been following the recent events in the trial.
They said: "The existence of such a person is difficult, if not impossible, to imagine and assurances that there is a rock at the FAA under which that person has been found should be greeted with the scepticism it plainly deserves."
In a new filing late on Friday, they asked Brinkema to order Martin to testify at a hearing to determine that the new witnesses had not been tainted.
Prosecutors are trying to prove that if Moussaoui had not lied to the FBI when he was arrested three weeks before 11 September, the attacks might have been prevented by heightened security efforts by the FAA.
Moussaoui, who was arrested after raising suspicions at a flight school, said he was not involved in the 11 September hijackings but was to take part in a second wave of attacks.
When he pleaded guilty, Moussaoui signed a statement that said he knew of al-Qaida's plans to fly aeroplanes into buildings in the United States.
Brinkema said the new aviation witnesses could testify about what the US government "could" have done to prevent the attacks if Moussaoui had told the FBI the facts that he admitted when he pleaded guilty.
Brinkema said: "The witness, or witnesses, may not, however, testify as to what the United States government 'would' have done with this information, as such testimony would be unduly speculative and misleading to the jury."
The trial resumes on Monday.