The Oxford professor issued a statement through his lawyer, Yassin Bouzrou, saying that he "categorically rejects all these false allegations."
Bouzrou added that Ramadan had filed a complaint "for slander and defamation" with the public prosecutor in Rouen.
According to Ayari, Ramadan raped the former Salafi writer after inviting her to his hotel room following a conference on Islam in Paris in 2012.
Ayari told the Telegraph on Saturday that she was surprised that he asked her to meet him in his room rather than the lobby, and she said that, once in his room, he put his arms around her and began kissing her.
The author previously wrote about the alleged assault in her book, "I Choose to Be Free," without providing the identity of the attacker.
"When I fought back and shouted at him to stop, he insulted me and humiliated me," she wrote, describing the assailant by a Muslim intellectual and speaker under the pseudonym Zoubeyr in a hotel room in Paris.
"I will not give precise details of the acts he did to me. It is enough to know that he benefited greatly from my weakness," she wrote.
The author first revealed the alleged rape incident on her Facebook page, following the Harvey Weinstein scandal.
"I have been silent for several years for fear that he might take vengeance," Ayari said, explaining that he had threatened to "take it to my children. I was afraid and I kept silent all this time."
Ayari continued to say that though she "may not have the same financial means as him to pay for lawyers and experts," she "will go to the end of this fight whatever it costs."