The previously secret documents also reveal that flying saucers were spotted over Glasgow on Christmas Day 2008 and in the run-up to that year's Hogmanay celebrations.
There were also reports of a spaceship that resembled a "giant frisbee" in Annan, Dumfriesshire, the following July, and of "fiery red flame-like objects" which "hovered about then disappeared" in Hamilton that October.
Former Prime Minister Gordon Brown was even drawn into the debate about the existence of UFOs, having been urged in writing to take a more active role on the issue.
The letter, written in 2008, and from a "ufologist" warned that "inspiring the electorate & winning the hearts and minds of the public" on alien spacecrafts would have to be done "in a professional manner & also handled subtly & seriously ... so as to avoid becoming a laughing stock".
In November 2009 a member of the MoD personnel based in Leuchars RAF base in Fife thanked a member of the public for reporting a "totally silent" object travelling "very slowly, in fact almost drifting" by a house in Winchburgh, West Lothian, adding: "It always amazes me how many UFO sightings there are in Scotland."
The 25 files, running to more than 4400 pages, were part of a tranche of UFO-related material released by the National Archives today. They cover the work carried out in the final two years of the MoD's UFO desk, from late 2007 until November 2009.
Included is a report on a man who claimed he had been "living with an alien". The man, whose name was not revealed, said "that he definitely has an alien amongst his mists [sic] ... things move around the house".
Another man left a message on the UFO hotline in January 2008 to say a spaceship had taken his dog, car and tent while he was camping with friends near Cardiff.
In another case, a woman who saw "two orange balls" hovering over her back garden in Coventry in July 2008 contacted the MoD to ask if she and her Springer spaniel "could be contaminated" as a result. UFOs were also spotted near several major UK landmarks, including the Houses of Parliament, Stonehenge and Blackpool Pier, according to the files.
The case files reveal that the MoD received a letter from a school pupil asking to be told the truth about UFOs after she reported seeing "strange" lights; and it also shows that the ministry rejected an offer of a weapon that could "shoot down UFOs".
In a twist that will delight conspiracy theorists, the number of sightings trebled in the year the MoD closed its UFO hotline.
While in the years between 2000 and 2007 just 150 reports a year were received, by November 2009 that number had jumped to 520, alongside another 97 freedom of information requests about UFOs.
Despite the jump in numbers the MoD decided to close its UFO desk, warning it was draining vital manpower from more important "defence-related" work.
Notes accompanying the released documents point to a rational explanation for the rise in reports. It notes that around the same time there was a surge in popularity in the use of Chinese lanterns, which when spotted from far away can share many of the characteristics of so-called UFOs.
In fact one sighting, in Leith in 2009, contains the note that the person who reported the sighting "states it could have been Chinese lanterns".