Germany said it had no choice but to supply a court with evidence that led to the release of a man on trial over the 11 September attacks.
Despite his release, Mr Mzoudi has not been formally acquitted
A Hamburg judge freed Abdelghani Mzoudi on Thursday after a secret source had testified he was not part of the cell that planned the suicide hijacks.
Prosecutors are now trying to prevent the conviction of another man on the same charge from being quashed.
Washington has suggested Germany failed to handle the Mzoudi case effectively.
Mr Mzoudi, a Moroccan was originally charged with being an accessory to the murders of more than 3,000 people who died in the attacks in New York and Washington.
The evidence which led to his release is widely believed to be based on testimony obtained from an al-Qaeda leader being held in US custody.
A spokeswoman for the German justice ministry said on Friday that the government had been obliged to pass on the testimony to the Hamburg court.
Under German law, the authorities are obliged to supply evidence which could favour a defendant.
"These documents were seen as material, or important, for this trial," the spokeswoman told a government news conference.
"How the court evaluates the evidence, the sources, the witnesses, is a matter for the independent court," she added.
A lawyer for another Moroccan convicted and jailed on identical charges as those against Mr Mzoudi, has said he will demand the immediate release of his client on the basis of the new testimony.
Mounir al-Motassadek is the only person convicted worldwide of a role in the 11 September attacks.
German prosecutors have sought to block the move and a ruling is expected on Monday.
The new testimony was submitted by Germany's Federal Criminal Investigation Bureau (BKA), which did not name its source.
According to the testimony, the so-called Hamburg cell which plotted the 11 September attacks consisted of three of the eventual suicide hijackers and Ramzi Binalshibh, a leading al-Qaeda suspect captured in Pakistan last year and now being held in US custody.
Both the judge and prosecutors agreed that such evidence could only have come from Mr Binalshibh under US interrogation.
The German Government has refused to hand over US transcripts of the interrogation to Mr Mzoudi's defence team.
Judge Klaus Ruehle ordered Mr Mzoudi's release on the grounds that the new evidence did not incriminate him.
US Attorney General John Ashcroft has described the release of Mr Mzoudi as disappointing and said the US had a different system for trying suspects while protecting national security.
"When we encounter a circumstance like they encountered in Germany, there are ways in which that is... resolved at a higher level," he said.
Although Mr Mzoudi has been freed from custody, he has still not been formally acquitted.
Mr Mzoudi shared a flat in Hamburg with Mohamed Atta, the suicide hijacker believed to have led the attacks.
He went to the same mosque, attended the same Islamic discussion group and witnessed Mohamed Atta's will.
But the prosecution did not manage to prove that he knew about the hijackers' plans.