Typhoon jets are stationed at Lossiemouth, and Kinloss currently has a unit of Puma helicopters to support the NHS during the lockdown.
The recent good weather is suspected to be a reason for the increase in the use of drones.
The RAF said a number of incidents had been reported to it, air traffic control and police, adding that people were likely to be breaking rules because they were unaware of the restriction zones.
Typhoons are still being flown out of Lossiemouth for “essential flights” to maintain crews’ training or in preparation for upcoming Nato operations.
Former RAF station Kinloss is now an army barracks, but is also currently a base for three RAF Pumas which have been made available to the NHS for medical evacuations.