The incident took place at 1500 GMT in the biodiesel part of Saipol's industrial site in the port city of Sete.
The factory was not in operation when the explosion occurred, as maintenance work was being carried out, the prefecture said, adding that activity at the port of Sete was continuing.
The fire was brought under control at 1610 GMT, Saipol said in a separate statement.
Some 200 people were evacuated protectively, the prefecture said. It said that a smoke plume was spreading to the sea but there was no risk for the population.
Saipol, part of oilseed group Avril, is France's largest biodiesel producer.
(Reporting by Gus Trompiz, Dominique Vidalon; Editing by Leslie Adler)
