Investigators say they have not ruled out espionage as a possible cause for the sighting, possibly connected to Russia's war against Ukraine.
The Bavaria State Criminal Police Office (LKA) said police had been informed about a drone flight above the Manching Air Base near the city of Ingolstadt on Sunday evening, with officers then able to detect up to 10 drones.
Although a police helicopter was requested for reinforcement, those responsible for the illegal overflights could not be identified.
It comes after a series of illegal drone flights were recorded over the military security areas in Manching and neighbouring Neuburg an der Donau in December.
Authorities suspect that the drones are being used to take pictures of military installations.
The LKA is hoping witnesses will provide information to identify those responsible for the drone flights.
The Munich Public Prosecutor General's Office, responsible for cases related to terrorism and extremism, has taken over the investigation.
Manching is home to the German military's Technical and Airworthiness Centre for Aircraft which tests aircraft ordered for the country's air force.
Neuburg is the base of the German Air Force's 74th Tactical Wing, which monitors southern German airspace using Eurofighter Typhoons.
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