Three flights to Malta were diverted to Catania and another to Palermo on Thursday after a military drone developed an engine problem on the airport's only operational runway.
The incident happened at 11.30am, according to sources.
The flights had been heading to Malta from London Gatwick, Newcastle, London Stanstead, and London Luton.
The drone is believed to be operated by Frontex for surveillance flights over the Mediterranean.
The runway was reopened once the drone was removed from the runway. The diverted flights are due in Malta early in the afternoon.
The airport's secondary runway is closed for maintenance.