Reaper drones controlled by military staff are based at the Lincolnshire base and in January four protesters were arrested there after cutting through security wire.
Earlier this summer the show was cancelled because of runway repairs.
The two-day airshow has in the past been attended by 150,000  spectators.
Future shows could be held at RAF Scampton, also in Lincolnshire, the RAF said.
But it said an air show could not take place there until 2017 at the earliest.
"The RAF appreciates that the cancellation of the air show at RAF Waddington will be a disappointment to many," the statement said.
"However it is hoped that the intent to establish an alternative air show at RAF Scampton is evidence of the RAF's commitment to maintain its traditional and modern links to 'Bomber County'."
Four protesters from the group End The Drone Wars were arrested in January on suspicion of aggravated trespass at RAF Waddington.
The Reapers, which have high-tech sensors and laser-guided weapons, are based in Iraq, Afghanistan and Syria but are controlled by military staff in RAF Waddington.
The annual airshow at RAF Waddington has been axed by the Ministry of Defence over "increased security concerns".