John Negroponte was ambassador to Honduras from 1981-1985. As such he supported and carried out a US-sponsored policy of violations to human rights and international law. Among other things he supervised the creation of the El Aguacate air base, where the US trained Nicaraguan Contras during the 1980's. The base was used as a secret detention and torture center, in August 2001 excavations at the base discovered the first of the corpses of the 185 people, including two Americans, who are thought to have been killed and buried at this base.

During his ambassadorship, human rights violations in Honduras became systematic. The infamous Battalion 316, trained by the CIA and Argentine military, kidnaped, tortured and killed hundreds of people. Negroponte knew about these human rights violations and yet continued to collaborate with them, while lying to Congress.