Officials briefed ministers on the sighting of a diamond-shaped object near Pitlochry, Perthshire, in 1990.
A memo suggested the media be told "no definite conclusions" could be reached.
The documents show officials were more concerned about secret weapons being developed by other countries rather than alien visitors.
The sightings were brought to the attention of the MoD by the Daily Record newspaper.
Witnesses reported seeing an object hanging in the air for 10 minutes before it ascended vertically at high speed.
The question is what are the Russians testing and could any of these sightings be something of that kind?
Dr David Clarke
Lecturer, Sheffield Hallam University
Military experts concluded the aircraft pictured was a Harrier, but could not identify the mystery object.
Fearing there could be significant media interest, officials provided ministers with guidelines for answering questions.
The memo noted there was no record of Harriers operating in the area at the time and suggested the media should be told: "no definite conclusions reached regarding large diamond-shaped object."
Drawings were later commissioned of the object with a note saying: "Sensitivity of material suggests special handling."
The seven files, produced by the DI55 branch of the Defence Intelligence Staff, contain details of 1,200 UFO sightings between November 1987 and April 1983. They include:
* A woman who was approached by an alien with a "Scandinavian-type accent" near Norwich in 1989.
* A spate of sightings in London in 1993, explained by the presence of an illuminated airship advertising the Ford Mondeo.
* Sightings by crews of six RAF Tornado jets of a UFO over Germany in 1990, believed to be a stealth aircraft.
Pilot death
They also reveal how the MoD abandoned a plan to computerise its records of UFO sightings in case it prompted public concern.
The files dismiss 1992 media reports that the death of a US Air Force pilot was caused by a UFO over the North Sea.
A local newspaper had reported that Capt William Schaffner's last radio messages referred to a conical shape followed by another shape "like a large soccer ball... made of glass".
The military investigation concluded he misjudged his height as he practised shadowing low-flying targets at night.
Dr David Clarke, UFO expert and journalism lecturer at Sheffield Hallam University, said the files showed the MoD was "not the slightest bit interested in aliens".
"They're only interested in the defence implications," he said
"The question is what are the Russians testing and could any of these sightings be something of that kind? As soon as they have eliminated that, they are not interested."
The files can be accessed at the National Archives website.(http://ufos.nationalarchives.gov.uk/)
Source: BBC News
