Pilots have apparently fired upon the unidentified objects without success since the 1980s, according to Nick Pope, who used to run the Ministry of Defence's UFO project.
"There was a faction in the MoD who said 'We want to shoot down a UFO and that will resolve the issue one way or another'," he told The Sun.
"We know of cases where the order has been given to shoot down - with little effect to the UFO."
Mr Pope claimed that the RAF only attempted to engage when the mysterious objects were perceived to be a threat.
He said: "In the case of UFOs, whether the object is causing a threat is very much a pilot's judgement call. The public won't know unless it comes down in a heavily populated area."
The MoD refused to comment.
Earlier this month, residents in the Lincolnshire Wolds were left puzzled by the destruction of a wind turbine within hours of several sightings of strange glowing orbs.
At least half a dozen residents reported seeing the orange-yellow spheres, which some witnesses claimed were trailing tentacles.
Dorothy Willows, who lives a mile and a half from the wind farm, said she saw a "low-flying object skimming across the sky towards the turbines" on January 4.
The following morning, a 213ft glass fibre turbine was left crippled, with locals reporting hearing a loud bang like thunder.
One of the £1 million turbine's 65ft blades was ripped off and another severely damaged
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