According to radio station France Bleu, the incident took place on the night of Tuesday, August 17.
According to the newspaper, one or more intruders broke into the building, overturning all the tables and computers there.
The vandals also removed ampoules with vaccines from the refrigerator, emptied them and scattered them on the floor.
About 500 doses of coronavirus vaccines have been destroyed.
The police launched an investigation.
Earlier it was reported that French law enforcement agencies used tear gas at a protest against sanitary passes in Lyon due to the outbreak of unrest.