The man who used to keep the Government's UFO files denied claims that the Queen, Margaret Thatcher and the Ministry of Defence covered-up official interest in crop circles.

Nick Pope, Britain's leading UFO expert, was responding to a report by West crop circle expert Colin Andrews, who claimed the Queen and the Duke of Edinburgh were fascinated by the phenomenon in the late 1980s and early 1990s.

Mr Andrews produced a letter from Prince Philip saying he believed the circles were made by some invisible force.

But Mr Pope said he was reading too much into Government interest at the time.

"He is implying I was involved in a cover-up. Some of the issues Colin highlights have arisen because the line between official and private interest – even within Government, the military and the intelligence agencies – can be blurred," he said.

"There are particular sensitivities and political difficulties when members of the Royal Family are involved. I agree that the MoD has downplayed its interest and involvement in the crop circle issue, as it has with the UFO phenomenon.

"This has been the policy for many years and it's no secret that I had to play my part in this when I worked for the Government."

The spat between the two experts has revealed more about the summer of 1989, when the world's attention was focused on Wiltshire as it appeared aliens were trying to communicate with the people of Warminster and Alton Barnes.

And Mr Andrews' royal theories overshadowed a more serious debate about what the Government knew about crop circles, and why it pretended not to be interested.

Wiltshire's fields and lanes were packed with Japanese and American TV news crews and the hilltops were full of crop circle devotees watching the fields at night.

Mr Andrews was the leading expert on the phenomenon at the time, and wrote the first crop circle book, which was on the Queen's summer reading list that year.

At the time, and for years since, the Government and the MoD denied they were interested in crop circles and what caused them. Prime Minister Margaret Thatcher dismissed the phenomenon and denied the MoD investigated them.

But Mr Andrews claims he was in constant communication with MoD officials and Whitehall. He said panicking MoD bosses gagged the media for a few hours when they thought they captured a crop circle being formed during Operation Blackbird in 1989.

Mr Andrews has released letters and documents which reveal the MoD investigated what caused crop circles and dealt with theories that military helicopters created them.

"Throughout the late 1980s and early 1990s military aircraft over crop circles were commonplace and witnessed by all who visited the circles. Military aircraft were witnessed taking photographs and manoeuvring over the formations regularly," he said.

Mr Andrews said he released his report to counter a "rewriting of history" by the Government and Mr Pope, its former UFO investigator, over official interest.

"I find it ironic that in the 1980s and 1990s I was accused of being a Government cohort due to the help I was given, and now I am accused of making up Government involvement," he said.