A drone was spotted over the Seine-Port marine transmission centre, which communicates with French navy submarines, at 9.30pm on Saturday.
The centre, which is south-east of Paris, houses several radio masts, some of them more than 200 metres high.
Air-transport gendarmes have been charged with investigating the incident.
Drones were spotted near a naval base in Brest, western France, that is home port to four nuclear submarines.
There have been at least 60 drone flights over sensitive sights and over Paris itself, where they are banned, since 5 October and the authorities have been unable to find any of the people responsible, apart from three Al-Jazeera journalists.