Klass's investigation of the MJ-12 documents found that Robert Cutler was actually out of the country on the date he supposedly wrote the "Cutler/Twining memo", and that the Truman signature was "a pasted-on photocopy of a genuine signature—including accidental scratch marks—from a memo that Truman wrote to Vannevar Bush on October 1, 1947". Klass dismissed theories that the documents were part of a disinformation campaign as "ridiculous", saying they contained numerous flaws that could never fool Soviet or Chinese intelligence. Other discrepancies noted by Klass included the use of a distinctive date format that matched one used in Moore's personal letters, and a conversation reported by Brad Sparks in which Moore confided that he was contemplating creating and releasing some hoax Top Secret documents in hopes that such bogus documents would encourage former military and intelligence officials who knew about the government's (alleged) UFO coverup to break their oaths of secrecy.

As early as the summer of 1987, spokesmen from the White House and National Security Council denied the existence of any organization called Majestic 12, MJ-12 or Majic-12.

On September 15, 1988, a special agent at the United States Air Force Office of Special Investigations (OSI) contacted the Dallas branch of the FBI after receiving the Majestic 12 document from an individual at an unnamed school who claimed to have received it in the mail. The FBI then began its own investigation of the supposed "secret" document and quickly formed doubts as to its authenticity. After receiving information from the OSI on November 30 of that year that no such committee had ever been authorized or formed, the FBI declared that the document was "completely bogus". The Director of the FBI subsequently instructed the Dallas office to close their investigation.

MuckRock contributor Emma Best has suggested that the papers were "government sponsored, or at least tolerated, disinformation" because the declassified FBI file on Majestic 12 does not mention any further investigation to find or prosecute the forger responsible for it.

In addition to the Roswell incident, the memo also mentioned a second UFO crash on December 6, 1950 in the vicinity of the towns of El Indio and Guerrero along the Mexico–US border. In an effort to determine the veracity of this claim (and in turn, the memo), UFO investigator Dennis Stacy and others made several trips to area in the early 1990s to seek evidence of whether such a crash had occurred. While he was able to find one local resident in Guerrero, Mexico who claimed to have witnessed the crash of a fireball followed several days later b…

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The following individuals were described in the Majestic 12 documents as "designated members" of Majestic 12.
• Lloyd Berkner
• Detlev Bronk
• Vannevar Bush
• James Forrestal
• Gordon Gray
• Roscoe H. Hillenkoetter
• Jerome Clarke Hunsaker
• Donald H. Menzel
• Robert M. Montague
• Sidney Souers
• Nathan F. Twining
• Hoyt Vandenberg

• Stanton T. Friedman, TOP SECRET/MAJIC, 1997, Marlowe & Co., ISBN 1-56924-741-2
• Philip J. Klass, The MJ-12 Crashed Saucer Documents, Skeptical Inquirer, vol XII, #2, Winter 1987–88, 137–46. Reprinted (sans figures) as chapter 7 of The UFO Invasion.
• Philip J. Klass, The MJ-12 Papers – part 2, Skeptical Inquirer, vol XII, #3, Spring 1988, 279–89.
• Philip J. Klass, MJ-12 Papers "Authenticated"?, Skeptical Inquirer, vol 13, #3, Spring 1989, 305–09. Reprinted as chapter 8 of The UFO Invasion.
• Philip J. Klass, New Evidence of MJ-12 Hoax, Skeptical Inquirer, vol 14, #2, Winter 1990, 135–40. Reprinted as chapter 9 of The UFO Invasion. Also reprinted in The Outer Edge: *Classic Investigations of the Paranormal, edited by Joe Nickell, Barry Karr, and Tom Genoni, CSICOP, 1996.
• Joe Nickell and John F. Fischer, The Crashed Saucer Forgeries, International UFO Reporter, March 1990, 4–12.
• Curtis Peebles, Watch the Skies: a Chronicle of the Flying Saucer Myth, 1994, Smithsonian Press, ISBN 1-56098-343-4, pp. 264–68.
• Carl Sagan, The Demon-Haunted World: Science as a Candle in the Dark, 1995, Random House, ISBN 0-394-53512-X, p. 90.
• Kathryn S. Olmsted, Real Enemies: Conspiracy Theories and American Democracy, World War I to 9/11. Chapter 6: Trust No One: Conspiracies and Conspiracy Theories from the 1970s to the 1990s. 2009 Oxford University Press. ISBN 978-0-19-975395-6