The verdict of the Federal Criminal Court is another setback for Lauber, who also faces a disciplinary probe into his conduct in the high-profile case just as he seeks re-election by parliament.
Lauber last month defended himself and said "conspiracy theories" over his meetings with FIFA President Gianni Infantino and presumptions of dishonesty were interfering with prosecutorial integrity.
Lauber has been investigating several cases of suspected corruption involving FIFA, based in Zurich, dating back to 2014 and the presidency of Sepp Blatter. The criminal probe treats FIFA as a victim rather than as a suspect.
Lauber had acknowledged two meetings with current FIFA president Infantino in 2016, saying they were intended to help coordinate the investigation. He later acknowledged a third meeting in 2017 after media reports of the encounter emerged.
The agency overseeing the Office of the Attorney General (OAG) had chided Lauber for not documenting the meetings with Infantino, exposing him to potential allegations of bias. That was also cited in the court's ruling released on Tuesday.
"The obligation to treat all parties to the proceedings equally and fairly and to grant them the right to be heard ... cannot be reconciled with the approach chosen by the Federal Prosecutor in the specific proceedings," the court said.
"Furthermore, although it plays only a subordinate role, the location of the meetings (restaurant, hotel) outside the premises of the Federal Prosecutor's Office chosen for 'clarification of case-related questions' is at least unusual."
The OAG said that it was analysing the court verdict.
Lauber's office has been involved in a number of sprawling, high-profile money laundering and corruption cases linked to Brazilian state oil firm Petrobras, Malaysian state development fund 1MDB and FIFA, but it has yet to bring charges.
(Reporting by Michael Shields; Editing by Hugh Lawson)
