His book The Reign of ETS: the Corporation That Makes up Minds, an investigation of the SAT I exam and its creators, the Educational Testing Service, was printed as part of the Ralph Nader report in 1980.

On November 12, 1991, covering developments in East Timor, Nairn and fellow journalist Amy Goodman were badly beaten by Indonesian soldiers after they witnessed a mass killing of Timorese demonstrators in what became known as the Santa Cruz Massacre.

[1][2] Nairn was declared a "threat to national security" and banned from East Timor, but he re-entered several times illegally, and his subsequent reports helped convince the U.S. Congress to cut off military aid to Jakarta in 1993.

In an article published in The Nation in 1994 Nairn revealed the U.S. government's role in establishing and funding the Haitian paramilitary, Front for the Advancement and Progress of Haiti (FRAPH) which was involved in human rights abuses.

[6] On April 19, 2017, the Intercept published an exposé researched and written by Nairn warning that a cadre of Indonesian military officers had joined forces with an ISIS-affiliated "vigilante street movement" in order to unseat President Joko Widodo.