The bureau has made thousands of files available in a new online resource called The Vault.
Among them is a memo to the director from Guy Hottel, the special agent in charge of the Washington field office in 1950.
In the memo, whose subject line is "Flying Saucers", Agent Hottel reveals that an Air Force investigator had stated that "three so-called flying saucers had been recovered in New Mexico".
The investigator gave the information to a special agent, he said.
The FBI has censored both the agent and the investigator's identity.
Agent Hottel went on to write: "They were described as being circular in shape with raised centers, approximately 50 feet in diameter.
"Each one was occupied by three bodies of human shape but only 3 feet tall," he stated.
The bodies were "dressed in a metallic cloth of a very fine texture.
Each body was bandaged in a manner similar to the blackout suits used by speed flyers and test pilots."
He said that the informant, whose identity was censored in the memo, claimed the saucers had been found in New Mexico "due to the fact that the Government has a very high-powered radar set-up in that area and it is believed the radar interferes with teh controlling mechanism of the saucers".
He then stated that the special agent did not attempt to investigate further.
The release of the secret memo is likely to fuel conspiracy theorists' claims of a government cover-up.
The town of Roswell in New Mexico became infamous after reports that a flying saucer had crashed in the desert near a military base there on or around July 2, 1947.
The bodies of aliens were said to have been recovered and autopsied by the US military, but American authorities allegedly covered the incident up
Military authorities issued a press release, which began: "The many rumours regarding the flying disc became a reality yesterday when the intelligence officer of the 509th Bomb Group of the Eighth Air Force, Roswell Army Air Field, was fortunate enough to gain possession of a disc."
The headlines screamed: "Flying Disc captured by Air Force."
Yet, just 24 hours later, the military changed their story and claimed the object they'd first thought was a "flying disc" was a weather balloon that had crashed on a nearby ranch.
Amazingly, the media and the public accepted the explanation without question. Roswell disappeared from the news until the late 1970s, when some of the military involved began to speak out.
Another memo published in The Vault from 1947 claimed that an object "purporting to be a flying disc" had been recovered near Roswell.
The disc was "hexagonal in shape" and "suspended from a balloon by a cable", according to the memo, marked as "Urgent", to the FBI director.
The memo noted that the disc resembled a weather balloon - but claimed that a telephone conversation between the Air Force and the field office "had not (word censored) borne out this belief".
The disc and balloon were being transported to Wright Field for further inspection, the memo noted.
It added that the information was being flagged up because of "national interest" in the episode, and noting that both NBC and the AP were set to break the story that day.