The report began:
The report's purpose was to warn other domestic law enforcement agencies to "the potential for extremist criminal activity in the United States by individuals or domestic groups who attach special significance to the year 2000." The report also stated: "The threat posed by extremists as a result of perceived events associated with the Year 2000 (Y2K) is very real. The volatile mix of apocalyptic religious and (New World Order) conspiracy theories may produce violent acts aimed a precipitating the end of the world as prophesied in the Bible."
The groups named as "potentially violent" were "biblically-driven cults," "militias, adherents of racist belief systems such as Christian Identity and Wotanism, and other radical domestic extremists." Regarding the "biblically-driven cults", the report warned that: "less time spent on “Bible study” and more time spent on “physical training” - indicate that the cult may be preparing for some type of action." The report ends by discussing possibility of terrorist attacks in the city of Jerusalem saying, "The extreme terrorist fringes of Christianity, Judaism, and Islam are all present in the United States. Thus, millennial violence in Jerusalem could conceivably lead to violence in the United States as well."
Insight on the News commented, "In a polemic presented as a threat report, the FBI has targeted religious groups and rightwing eccentrics as potential terrorists likely to go postal as the new millennium arrives...Even at the height of the Cold War during the seventies and eighties the FBI was not allowed to pursue openly declared revolutionary Marxists in this way, being required by the courts to show cause by establishing an actual attempt to commit illegal acts.
The American Civil Liberties Union, ACLU, cited Project Megiddo in its defense of filmmaker Mike Zieper. His film about a military takeover of Times Square was removed from the Internet due to FBI pressure. On November 10, 1999 the International Asatru-Odinic Alliance accused the F.B.I. of violating its First Amendment rights to freedom of religion, free speech, and peaceful assembly. The reason given for this accusation was the propagation of numerous false statements and innuendos about Odinism in the Project Megiddo report.