Management at a nuclear power station in Saint-Alban on the river Rhone called in police after a drone flew over the site on Thursday, although they insisted that the flight had had no effect on its operations or its security.
Another flight was reported over an industrial and research centre in Marcoule.
At least 17 flights by drones over nuclear power stations have been reported the beginning of October without police finding out who is responsible for them.
As many as five flights have taken place on the same night, leading to speculation that they are part of an organised campaign but anti-nuclear groups have denied responsibility and no-one else has confessed.
Officials did not admit publicly the flights were taking place until 24 days after the first on 5 October and are anxious to calm public fears over security.
Two men and a woman were arrested near a power station at Bellevile-sur-Loire in central France on Wednesday and the men have been charged with flying an apparatus in a restricted area.
But the public prosecutor announced on Friday that they were just modelling enthusiasts who wanted to film a boat they had made on the lake next to the plant.
On Wednesday Environment Minister Ségolène Royal assured parliament that everything was being done to protect France’s nuclear installations.