In the early 1960s, Shackley's work included being station chief in Miami, during the period of the Cuban Missile Crisis, as well as the Cuban Project (also known as Operation Mongoose), which he directed. He was also said to be the director of the "Phoenix Program" during the Vietnam War, as well as the CIA station chief in Laos between 1966–1968, and Saigon station chief from 1968 through February 1972. In 1976, he was appointed Associate Deputy Director for Operations, second in charge of CIA covert operations.