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While most reports of flying saucers are quickly dismissed by defence chiefs, the previously classified papers show the sighting, which took place near Pitlochry in 1990, was taken extremely seriously. A former MoD official who investigated the case told Scotland on Sunday that despite strenuous efforts they could find no earthly explanation for the craft.
Witnesses reported seeing a large, diamond-shaped object hanging in the air next to a RAF Harrier above the A9 at Calvine, north of Pitlochry, on August 4. The UFO is said to have hovered for about 10 minutes before zooming skywards at high speed and disappearing from view.
The apparent close encounter of the Caledonian kind was photographed by members of the public whose images appear to show a blurry, diamond-shaped craft next to a jet. Fearing the pictures would spark significant media interest, the MoD decided to bring it to the attention of the Government. A Whitehall official wrote in a memo: "Such stories are not normally drawn to the attention of ministers. "On this occasion, however, the MoD has been provided with six photographic negatives of an alleged UFO... and has been asked for comments almost certainly for inclusion in a forthcoming story."
The memo suggested the media should be told that "no definite conclusion had been reached regarding the large diamond-shaped object". It has also emerged the MoD went on to commission a series of line drawings of the object the following year, noting that the "sensitivity of the material suggests very special handling". Former MoD civil servant Nick Pope, who dealt with UFO reports, described the image as the "most impressive" ever shown to his department.
He said: "The MoD has all sorts of equipment and expertise that we used to analyse and enhance imagery to tell whether there were any signs of fakery.
"This picture was assessed by our digital experts, who concluded it was a real photograph showing a solid-structured craft which was estimated as being around 25m in diameter. There were no wings and no visible signs of any propulsion system. It was exotic and unknown in a way far beyond even the most modern stealth aircraft being trialled at that time."
Pope, who served in the MoD for 21 years until 2006, claims they were unable to come up with any firm answers about the craft and its origins.
"I remember going to a briefing with the defence intelligence staff where the photograph was discussed. My opposite number in defence intelligence pointed his finger to the left and said, 'It is not the Americans,' then to the right, saying, 'It is not the Soviets,' and finally, he said, 'That only leaves...' and pointed his finger directly up."
During his time with the ministry, Pope had a blown-up copy of the photograph on his office wall until it was personally taken down by his superior. He recalled: "My head of division removed it and put it in his drawer because he was convinced, wrongly in my opinion, that it showed a top secret prototype craft.
"Somewhere along the line the photo disappeared, but I have no idea whether it was genuinely misplaced or whether it was treated as something we shouldn't have seen and put through a shredder."
Meanwhile, another newly released file reveals how efforts to create a computer database of UFO reports were halted amid fears of a potential public relations disaster should its existence come to light. The aim was to produce a database which could supply information and explanations when ministers were asked questions in Parliament about sightings.
A memo from March 1988 revealed the project was to be ditched because it "contravened" statements from ministers saying UFOs did not pose a threat to the UK. The official wrote: "I also understand that there was some concern about public reaction if knowledge of the work being undertaken emerged in the media."
A further file insists that the death of an US Air Force pilot attached to the RAF was a "tragic accident" rather than the result of a UFO encounter. Captain William Schaffner's fatal crash into the North Sea on September 8, 1970, made headlines over allegations he was on an secret operation to intercept a glowing, unidentified craft. But an MoD report concluded: "There is no reason to suggest that there is any sort of UFO incident in any way connected with the tragic crash."