Six swastikas were drawn on the front of the mosque at Provins, in the Seine et Marne department outside the French capital.
The attack comes just a week after several mosques across France were also targeted with similar Islamophobic graffiti.
The symbols at the Provins mosque were discovered by worshipers when they turned up for morning prayers on Saturday.
A complaint was immediately filed with police.
In a statement, the Regional Council of the Muslim Faith for the region of East Ile-de-France "condemned the act in the strongest terms" and called for Muslims to be “vigilant and peaceful in the face of despicable and cowardly acts of provocation ".
Marwan Muhammad from the Collective against Islamophobia in France told The Local the current anti-Muslim climate in France was fueling the recent attacks.
“Muslims are being stigmatized and presented as a problem in France,” he said. “Negative signals are being sent out by politicians, including those on the left and this helps to empower people to take action.
“Police need to find them and punish them in the strongest way possible. They need to send a message that people cannot get away with this.
Muhammad told The Local that with each attack against a mosque fears are rising among the country’s Muslim population.”
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“People are contacting us on a daily basis at the moment. We are trying to calm them down and tell them to have faith in the police,” he said.
“The worst thing that is happening is some people are saying we just have to hide away and tolerate it.”
France’s Interior Minister Manuel Valls also “strongly condemned the intolerable act” and vowed the authorities would come down hard on the perpetrators. Valls “understands and shares the emotion” of the Muslim community,” the ministry said in a statement.