Inscriptions reading "Islam get out of Europe", "No to Islam and to burkas", along with swastikas, were discovered on Wednesday in Herouville-Saint-Clair, a suburb of the city of Caen in Normandy.
The incident came a day after French lawmakers passed on first reading a bill banning women from wearing the full-face Islamic vail in public.
Immigration Minister Eric Besson called the vandalism "cowardly" and "foolish".
"I cannot begin to describe my indignation," the minister said. "France has always been, and will remain, a land of immigration and integration."
Similar incriptions were discovered in May at a hallal butchery in Lisieux, also in Normandy.
Several other mosques and Muslim cemeteries have been marked in recent months, the minister said in a statement.