The drone was seen late Saturday over a base in Seine-Port from which France's navy communicates with its submarines.
Drones have been seen over several high-profile areas of the French capital in recent weeks, as Paris remains on high alert after three gunmen killed 17 in three days in January.
Mysterious sightings have been made near the US embassy, not far from the Invalides military museum, the Eiffel Tower and several major thoroughfares leading in and out of the French capital, police said.
Police have been unable to catch any of the operators of the night-time flights and it is unclear whether they are the work of pranksters, tourists or something more malicious.
French authorities were first alerted to mystery drone flyovers in October, when state-run power company EDF filed a complaint with police after detecting the small aerial vehicles zipping over seven atomic plants across the country.
The sightings continued into November, and altogether some 20 flyovers took place over nuclear plants. Their operators were never found.
Then on January 20th, a pilotless aircraft briefly flew over the presidential palace in Paris, shortly after the jihadist killings.
And in late January, small drones were also spotted near a bay in Brittany that houses four nuclear submarines -- one of the most protected sites in the country.