Helena Costa said she quit her job as Clermont coach because she found out players were hired without her consent.
The 36-year-old also accused the French second division club of "total amateurism" and a "lack of respect".
The Portuguese added: "For any leader in an organisation who is responsible for a team, it's unacceptable."
Costa was the highest-profile female manager to be put in charge of a men's team in European football when she was appointed in May.
In a joint news conference on Tuesday morning to explain her departure, Costa said she was leaving for "personal reasons" while president Claude Michy said her decision was "astonishing and incomprehensible".
"She's a woman," added Michy. "They are capable of leading us to believe in certain things."
Costa, who had previously coached the Iran women's national team and scouted for Scottish Premier League club Celtic, subsequently decided to issue a statement clarifying her reasons for leaving.
She explained that the club's sporting director did not reply to any of her emails during a five-day period and claimed she tried to take the case to the club president but could not talk to him either.