Swiss prosecutors have launched legal proceedings against Fifa president Gianni Infantino.
It is in relation to an alleged secret meeting the head of world football's governing body held with the Swiss attorney general Michael Lauber.
Lauber last week offered to resign after a court said he covered up the meeting and lied to supervisors during an investigation by his office into corruption surrounding Fifa.
Both have denied any wrongdoing.
Fifa said Infantino and the governing body would "co-operate fully with this investigation".
In a statement released through Fifa, Infantino said: "As president of Fifa, it has been my aim from day one, and it remains my aim, to assist the authorities with investigating past wrongdoings at Fifa. Fifa officials have met with prosecutors in other jurisdictions across the world for exactly these purposes."
Fifa also highlighted a comment Infantino made in June, when he said: "To meet with the attorney general of Switzerland is perfectly legitimate and it's perfectly legal. It's no violation of anything."
Lauber's office said he officially tendered his resignation on Tuesday, with his last day of active duty set for 31 August.
It comes after special prosecutor Stefan Keller was appointed in June to review criminal complaints against the two men and others.
He found indications of criminal conduct related to their meetings, the authority overseeing the Office of the Attorney General (OAG) said.
"This concerns abuse of public office, breach of official secrecy, assisting offenders and incitement to these acts," the watchdog overseeing the OAG said in a statement.
The OAG said it had taken note of the development, adding Lauber would make statements to parliamentary committees if necessary.
The watchdog said Keller had now opened proceedings against both Infantino and a regional public prosecutor who was involved in the meetings, and was seeking parliamentary approval to have Lauber's immunity from prosecution waived.
Fifa is based in the Swiss city of Zurich.