A spokesman for security forces said: "Drone-type machines overflew two nuclear plants during the night. They were detected by police in charge of protecting the plants and staff."
"These machines were not neutralised because they did not represent a direct threat" to the nuclear facilities, the spokesman added.
National energy company EDF said on Wednesday it had identified seven drones flying over its plants this month and had filed a complaint with the police.
A spokeswoman for EDF confirmed the latest incident, which she said happened around 9:00 pm local time over plants at Penly in northern France and Golfech in the southwest.
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The drone flights have sparked questions over security of nuclear plants in France, which relies heavily on nuclear energy for electricity.
The interior ministry has stressed that a drone does not pose any concern for the plants which are "designed to withstand a strong earthquake or an airliner crashing into it."
It is against French law to fly within a five kilometre radius of a nuclear plant. Those breaking this law are liable to one year in prison and a fine of USD 93,000.
France, the world's most nuclear-dependent country, operates 58 reactors and has been a leading international cheerleader for atomic energy.
But in a deal with the Greens before the 2012 parliamentary and presidential elections, President Francois Hollande's Socialist party promised to cut reliance on nuclear energy from more than 75 per cent to 50 per cent by shutting 24 reactors by 2025.