From August 1983 until November 1987, Gaffney held the position of Deputy Assistant Secretary of Defense for Nuclear Forces and Arms Control Policy in the Reagan administration, again serving under Perle.

[26] In December 2015, Nation Institute Fellow Eli Clifton characterized as unscientific a CSP-funded poll that Donald Trump had been citing, which purportedly showed widespread support for Sharia law among U.S. Muslims and a need for intervention in that community.

[27] Discussing what he calls prominent professional participants in Islamophobia, Professor Todd Green wrote mentioned "Frank Gaffney and David Yerushalmi, both of whom head organizations that are responsible for spreading misinformation about Islam and that seek to enact anti-Muslim laws, including the infamous anti-Sharia".

David Yerushalmi served as legal counsel for the CSP[28] and has been accused of spreading misinformation about Islam and encouraging the enactment of anti-Muslim laws, including anti-Sharia legislation in the United States.

[36] Reporting on the allegation, the Bulletin of the Atomic Scientists observed that, following its publication, "fax machines around Washington, D.C., and across the country poured out pages detailing Russian duplicity.

[43] The Anti-Defamation League has said that Gaffney "has promulgated a number of anti-Muslim conspiracy theories over the years" and that he has "undue influence" relative to other like-minded figures.

[44] Other commentators have suggested that Gaffney's propensity for conspiracy theories began earlier during his career in the Reagan administration, where after being denied a higher position, was convinced that Soviet agents within the United States government were blocking him.

[45] One of Gaffney's main conspiracy theories is the so-called "Civilization Jihad", a supposed secret Muslim plan to take over America, which came to national prominence by being cited in a debate by 2016 presidential candidate Ben Carson.

[46] According to the SPLC, Gaffney's beliefs stem "from a single discredited source – a 1991 fantasy written by a lone Muslim Brotherhood member that was introduced into evidence during the 2008 Holy Land Foundation trial in Dallas federal court.

[47] The ADL quotes Gaffney as "mentioning that in 1991, a Muslim Brotherhood operative produced the "explanatory memorandum on the general strategic goal of the group in North America."

According to Gaffney, the memo explicitly addresses the progress the Muslim Brotherhood has made in building an infrastructure in the United States with the goal of destroying Western civilization from within so that Islam is victorious over other religions".

ACU chairman David Keene released a statement contending that Gaffney "has become personally and tiresomely obsessed with his weird belief that anyone who doesn't agree with him on everything all the time or treat him with the respect and deference he believes is his due, must be either ignorant of the dangers we face or, in extreme case, dupes of the nation's enemies".

[45] The column came two months after Gaffney unexpectedly left The Washington Times for Breitbart News, where he was a staff columnist and Keene was the opinion editor.

[53] Gaffney has been called a conspiracy theorist by Dave Weigel writing in Reason magazine;[54] Steve Benen of MSNBC;[55] Slate;[56] and The Intercept,[57][58][59] among others.