With a civilian population haunted by the Blitz and the Second World War still in the balance, it was one development Winston Churchill could have done without – an incursion into British airspace by an arrow-shaped metallic object feared to contain an invasion force of little green men.

Such was the sensitivity of an alleged UFO sighting by an RAF bomber crew returning to England from a mission over Germany that Churchill ordered it to be covered up with the words: "This event should be immediately classified since it would create mass panic amongst the general population and destroy one's belief in the Church."

This at least was the allegation put to the Ministry of Defence by relatives of a senior British military aide who claimed to have witnessed the cigar-chomping Prime Minister discuss the incident with General Dwight Eisenhower as part of a meeting about a succession of "foo fighter" sightings by Allied air crews in the Second World War.

The curious matter of visits by wartime aliens is one of hundreds of reports of strange celestial phenomena – from a space station covered in pulsating lights to an unusually agile rocket which buzzed a Boeing 737 at Manchester Airport – to be revealed in documents released today by the National Archives in Kew, west London.

The files are the latest tranche of 11,000 UFO sightings logged by the British Government between the early 1900s and 2000 to be released from Ministry of Defence files, providing a candid insight into a national obsession with suspected flying saucers and attempts by Whitehall functionaries to explain that they were – almost always – nothing of the sort.

Officials launched a investigation into the MoD files when the unnamed grandson of the British military aide to Churchill wrote in 1999 saying that the object seen by the RAF reconnaissance crew "appeared to hover noiselessly relative to the aircraft". The grandson, who described himself as a scientist, said: "It appeared metallic... the object very suddenly disappeared, leaving no trace of its earlier presence."

He added: "This event was discussed by Mr Churchill and General Eisenhower, neither of whom knew what had been observed. There was a general inability for either side to match a plausible account to these observations... another person raised the possibility of an unidentified flying object, at which point Mr Churchill declared the incident should be immediately classified for at least 50 years and its status reviewed by a future prime minister."

Video: Truth in UFO files?

Any decision by Churchill to halt publicity about the sightings has also gone unrecorded but in July 1952, after a spate of reports in Britain and the US, he wrote to the Air Ministry saying: "What does all this stuff about flying saucers amount to? What can it mean? What is the truth?" Unknown to Churchill, intelligence chiefs had formed The Flying Saucer Working Party in 1950 to investigate the reports, with the blessing of Lord Mountbatten, who thought the UFOs were alien craft.