The files are believed to date from 1971-76, 1996-2000 and 2004.
The release marks the final stages of what's been a nine-year long project to declassify and release the MoD's entire archive of UFO files.
Three of these documents have still not been released.
This prompted claims of a conspiracy to cover-up the existence of alien life among some theorists and another delay in publication last year added to this speculation.
"I think these files perfectly capture the wonder and fascination of the UFO mystery and show how MoD officials - myself included - struggled to make sense of one of the great mysteries of the modern era," said Nick Pope, who was part of the Ministry of Defence's UFO project from 1991 to 1994.
"Sadly, there's no 'smoking gun' in these files that will prove we've been visited by extraterrestrials, but there are plenty of intriguing UFO reports, as well as policy papers explaining how the MoD handled this subject."
"The lack of a smoking gun and the fact that these files seem to have been slipped out without a formal media announcement is bound to start some conspiracy theories, and I know that many people believe the 'good stuff' is being held back," he said.
Conspiracy theorists are hoping the files may shed light on the notorious Rendlesham Forest incident in 1980, dubbed Britain's Roswell.
Strange lights were reported by servicemen in the forest near RAF Bentwaters and RAF Woodbridge.
The disputed sightings, over three nights between December 26-28, occurred when Britain and the West were on high alert during the Cold War.
"What's readily apparent from a detailed study of all this is that the MoD was telling Parliament, the media and the public that the UFO phenomenon was of "no defence significance" and of limited interest to the MoD', said Mr Pope.
"However, the files show that behind the scenes, the subject was obviously taken more seriously than we let on, with many of the cases self-evidently being of great defence significance - e.g. when UFOs were seen in close proximity to military bases, were encountered by RAF pilots, or were tracked on radar by fighter controllers or air traffic controllers."
The remaining three files are due to be released later this year.
"This is a good day for open government and for freedom of information", Mr Pope said.
The last batch of files that was released contained some papers relating to anti-gravity and gravity modification research expressed by MoD scientists.
"I wasn't joking when I referred to MoD's UFO project as being 'the real-life X-Files'", said Mr Pope.
