The report was submitted to the Paris public prosecutor following testimony from Sonia Souid, an agent for several French internationals, during an audit of the French federation (FFF).
Sports minister Amelie Oudea-Castera said she had been informed by the head of the auditing body that a report had been made in accordance with the criminal code.
Le Graet, 81, was forced to step down as FFF president last week until the completion of the audit.
In a statement to AFP on Saturday, he said he was stunned by leaks to the media.
"I have just read with astonishment an article in Le Monde reporting leaks in the provisional audit report being prepared," he said in a statement. "At this stage, I know neither the facts of which I am accused nor the people who are behind them. More generally, I am surprised that information can be disclosed even though the interim report has not yet been sent to me and I have not been able to submit my observations."
During interviews with sports daily L'Equipe and broadcaster RMC, Souid accused Le Graet of unwanted sexual advances, claiming she felt "the only thing that interested him, and I apologise for speaking vulgarly, are my breasts and my ass."
In French law, "sexist outrage" refers to a statement or behaviour with a sexual or sexist connotation which undermines a person's dignity or exposes him or her to a distressing situation.
The offense can be punished with a fine of up to 750 euros.
Le Graet, in charge of the FFF since 2011 and with a mandate due to run until 2024, had faced calls to resign after what he admitted were "clumsy remarks" about Zinedine Zidane's potential interest in coaching the French national team.
He had said "wouldn't even have taken his call" when asked whether Zidane, a World Cup winner as a player and an all-time France great, had rung him to express an interest in taking over as coach from Didier Deschamps.
Deschamps, who led France to World Cup glory in 2018 and oversaw the run to last month's final which Les Bleus lost on penalties to Argentina, last week signed a new contract to stay as France coach until 2026.
© Agence France-Presse