At least five incidents were reported over central Paris by witnesses and police, a police source told AFP, confirming a report on Europe 1.
Police had already been trying to find out who was behind the appearance of an estimated five separate drones the previous night.
According to Europe 1 radio two or three drones were seen in the air around Place de la Concorde, while BFM TV said drones were also spotted above the Porte de Clignancourt, the Porte de Saint Ouen and Issy Les Moulineaux, all on the edge of Paris.
According to reports, eye witnesses and police were able to film the drones as they passed over head.
The images are being studied by a team of ten investigators from the French Gendarmerie’s specialist aviation unit (GTA), which was put together after the five drones were spotted flying above Paris in the early hours of Tuesday morning at specific locations such as the US embassy.
The question of who is flying the drones and whether their motives are malicious, remain a mystery for the moment.
"Is it a game? Scouting for future operations? The investigation will show us," a Parisian police chief said Tuesday.
Criminologist and air safety expert Christophe Naudin told The Local he believes it’s the work of so-called “eco-terrorists”.
My hypothesis would be that it is some kind of ‘eco-terrorist’ group, who want to demonstrate how the state is incapable of reacting against this new kind of threat,” he said.
“It appears to have been a very well organised operation, involving several drones, that may have been operated manually or on pre-programmed flights,” he said.
“It was done to ridicule the state and the forces of law and order and to show they are not capable of protecting the population.”
Naudin said there's no need to panic at the moment as terrorists are not trained to use drones, and the machines are not sophisticated enough to carry explosives, but in a few years time that will be different.
"One day they will be used for something dangerous," he said
The latest flyovers follow a series of drone spottings at French nuclear plants and, more recently, over the presidential palace.
The fresh sightings also come at a time of heightened security in Paris following last month's jihadist attacks that left 17 people dead.
French law bans small civilian drones from areas such as nuclear facilities which are protected by a no-fly zone that spans a 2.5-kilometre radius and a height of 1,000 metres.
Flying the unmanned aerial vehicles over the French capital is also banned by law.
In October, a 24-year-old Israeli tourist spent a night in jail and was slapped with a 400-euro ($450) fine for flying a drone above the Notre Dame cathedral.
Experts say that the small unmanned craft would not pose a threat if they crashed into a hardened nuclear facility, whose reactors are built to withstand the impact of mid-sized commercial planes.
But the country has nevertheless launched a one-million-euro ($1.1-million) programme aimed at developing ways of detecting and intercepting them.
The most basic drones are radio-controlled by someone nearby, but other more sophisticated models can be pre-programmed, and these are widely available for just €350 to €400 ($440 to $500).
Despite it being forbidden, spectacular videos have been posted on YouTube that appear to have been shot using a drone, like this one below, posted in March last year.