The chaos began when the two topless women race on to the stage as two Imams were giving a talk on Saturday evening at the conference in Pontoise near Paris.
The women, who were of Algerian and Tunisian origin, had anti-Muslim slogans on their chest that read: “No one will submit me, I am my own prophet". They began shouting the same words to the audience.
While the two Imams were clearly taken aback and stood back from the women, a group of around 15 men, including security guards, ran onto the stage to bring an abrupt and violent end to the protest act.
Images show the two women disappearing under a sea of bodies, with some of the men appearing to launch kicks and slaps at the pair. The melee continued behind a screen out of sight of the cameras.
The site Buzzfeed France confirmed that one of the women had been punched several times in the aftermath of the incident.
Police quickly intervened to lead the two women away.
While the organisers of the conference have announced their intention to file charges, the head of Femen Inna Shevchenko has defended the protest.
Fin du salon musulman pour ce samedi et retour au calme après l'irruption des FEMEN pic.twitter.com/CWAJPmdvtp— David Perrotin (@davidperrotin) 12 Septembre 2015
“The two Imams were in the process of discussing whether or not you should beat your wife,” said Shevchenko, explaining the reason the two women chose to act then.
She said there were cries of “dirty whores and kill them,” as the men stormed the stage. Shevchenko, who was at the event later, tweeted: "Femmophobia is illegal, sexism is racism and modern slavery is a crime".
The conference itself was controversial, with a petition to prevent it gaining around 6,000 signatures.
The petition denounced the presence of radical speakers including Nader Abou Anas, who has been accused of trying to legitimise rape within marriage.
Femen's provocative protests have prompted a violent response in the past notably when they disrupted an anti-gay marriage protest in Paris.
The video below shows how they were attacked by protesters, many of whom came from hardline Catholic groups and far-right organisations.