From 1981 to 1985 Negroponte was the U.S. ambassador to Honduras, given the title "proconsul". During this time military aid to Honduras grew from $4 million to $77.4 million a year, and the US began to maintain a significant military presence there, with the goal of providing a bulwark against the socialist Sandinista government of Nicaragua.
The previous U.S. ambassador to Honduras, Jack Binns (who was appointed by President Jimmy Carter) made numerous complaints about human rights abuses by the Honduran military and claimed he fully briefed Negroponte on the situation before leaving the post. When the Reagan administration came to power, Binns was replaced by Negroponte, who has consistently denied having knowledge of any wrongdoing.
Negroponte supervised the construction of the El Aguacate air base where Nicaraguan Contras were trained by the U.S., and which some critics say was used as a secret detention and torture center during the 1980s. In August 2001, excavations at the base discovered 185 corpses, including two Americans, who are thought to have been killed and buried at the site.
Negroponte is suspected by some commentators to have known of human rights abuses carried out by CIA-trained operatives in Honduras in the 1980s. Records show that a death squad, euphemized as a "special intelligence unit" of Battalion 3-16 of the Honduran armed forces, kidnapped, tortured and killed hundreds of people, including U.S. missionaries. This death squad was trained by the CIA, the Argentine 601st Intelligence Battalion and the Argentine Army Intelligence Service. Critics charge that Negroponte knew about these human rights violations and yet continued to collaborate with the Honduran military while lying to Congress.
In May 1982, a nun, Sister Laetitia Bordes, who had worked for ten years in El Salvador, went on a fact-finding delegation to Honduras to investigate the whereabouts of thirty Salvadoran nuns and women of faith who fled to Honduras in 1981 after Archbishop Óscar Romero's assassination. Negroponte claimed the embassy knew nothing about the nuns. However, in a 1996 interview with The Baltimore Sun, Negroponte's predecessor, Jack Binns, said that a group of Salvadorans, among whom were the women Bordes had been looking for, were captured on April 22, 1981, and savagely tortured by the DNI, the Honduran Secret Police, and then later thrown out of helicopters alive.
In early 1984, two American mercenaries, Thomas Posey and Dana Parker, contacted Negroponte, stating they wanted to supply arms to the Contras after the U.S. Congress had banned further military aid. Documents show that Negroponte brought the two together with a contact in the Honduran armed forces. The operation was exposed nine months later, at which point the Reagan administration denied any U.S. involvement, despite Negroponte's introductions of some of the individuals. Other documents detailed a plan of Negroponte and then-Vice President George H. W. Bush to funnel Contra aid money through the Honduran government.
http://en.wikipedia.org/wiki/John_NegroponteHe was ambassador to Iraq in 04-05 when the post invasion black ops were being set-up.