While at the CIA, Cannistraro ran the agency's Central American task force that supervised covert action in the region, including the Nicaraguan Contras (both the left wing guerillas in the South and the right wing contras in the North). He moved to the Reagan NSC by the direction of CIA Latin American Chief Duane Clarridge, who supported Col. Oliver North.[5] The Contra program was transferred in 1984 by President Ronald Reagan to the NSC,[6] and Cannistraro was made Director of Intelligence there later that year.[1] As director, he was responsible for monitoring the US intelligence community budget.[7] and coordinating the approval process for covert action. He also chaired the Afghanistan Working Group at the White House.[8]
In 1988, Cannistraro became Chief of Operations and Analysis at the CIA's Counterterrorism Center,[9] where he led the agency's investigation into the 1988 bombing of Pan Am Flight 103 over Lockerbie.
Cannistraro also alleged that Iraqi intelligence agent Farouk Hijazi had invited bin Laden to live in Iraq during a December 1998 meeting in Afghanistan, though he maintained that bin Laden refused the invitation and did not accept support from Saddam Hussein.[10]
He reported on the forged Niger "yellowcake" uranium documents as an attempt by some Bush administration supporters to link Iraq with nuclear weapons development in order to increase public support for the Iraq war), and on the related disclosure of the identity of CIA case officer Valerie Plame.[11]
The front company, Brewster Jennings & Associates, apparently also was used by other CIA officers whose work now could be at risk, according to Cannistraro.
Cannistaro runs IntelligenceBrief, a security and information service for private clients. The Vatican is one such client.[citation needed]
On September 12, 2001, Cannistraro stated that five of the hijackers had entered the United States in Maine from Canada via Yarmouth, Nova Scotia, and/or a remote border point near Jackman, Maine, several hundred kilometres southeast of Quebec City.