The masks were pilfered from a part of Conception hospital that is accessible only to staff and patients who have undergone surgery, the Marseille hospitals authority (AP-HM) told French news agency AFP.
"The AP-HM immediately launched an internal investigation to find the culprits," it said.
It assured that the hospital had enough masks to continue operations as normal, but that it had ordered more and taken steps to secure its stocks of both masks and sanitising hand gels.
News of the theft came as President Emmanuel Macron announced that the authorities would requisition all face mask stocks and production in response to the coronavirus outbreak.
Macron said they would be reserved for coronavirus patients and health professionals.
Four people have died of the virus in France, which has 204 confirmed cases of the disease.
Face masks have also caught the eye of thieves in Japan, who made off with some 6,000 masks from a hospital in the western city of Kobe in mid-February.
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