The spokesman said the security centre at the Mechernich site had reported the sightings to the police on Thursday, confirming reports in the German press. Officers had opened an investigation, the spokesperson added, declining to elaborate.
Mechernich is a special army site for storing equipment at a depth of 130 metres (425 feet) across some 30,000 square metres, or the equivalent of four football pitches.
It houses components for US-made Patriot air-defence systems, which Ukraine has frequently requested to help fight off Russia's aerial bombardments.
The latest incident comes days after an explosives-laden drone was found near a Ukrainian cargo plane at Leipzig-Halle airport, which plays a key role in the transport of military goods by the German military and NATO allies.
Various European countries have reported drone sightings above sensitive sites in recent years, with many leaders blaming Moscow at a time of high East-West tensions as a result of Russia's invasion of Ukraine.
