The alert came days after the Civil Aviation Authority issued a warning about the dangers caused by hobby aircraft.
The CAA revealed an Airbus’s wing passed around 20ft below a drone hovering at Heathrow earlier this month.
Now BAE Systems – which is developing unmanned military drones – has revealed a recent incident at its Warton site.
Paul Stone, Director of Flight Operations at BAE Systems Military Air and Information, said: “We are aware of an incident involving a remotely controlled drone at our Warton site.
“Our security team has been working closely with Lancashire Police to ensure this matter was dealt with effectively and swiftly.
“Our Warton aerodrome is a secure military site, and for this reason, the monitoring by external people of any part of the site, whether intentionally or otherwise, is something we take very seriously.
“In addition to this, the site is also an active airfield and the flying of remotely controlled drone poses a serious safety risk to aircraft using our site, their occupants and the local community.
“Fortunately, the incursion did not cause a safety risk on this occasion, but the proliferation of small Unmanned Air Vehicles (UAVs) and the risk of collision that this brings is a genuine concern.”
Lancashire Police said officers traced a 56-year-old man from Freckleton who voluntarily spoke with officers about the incident.
The matter was to be resolved through restorative justice.
“The man will be meeting with representatives from BAE as part of this in due course,” said the spokesman.