http://www.fpif.org/republicanrule/officials_body.htmlexcerpt:
But it was during his tour as ambassador to Honduras that Negroponte earned his reputation for being soft on human rights abuses. From 1981 to 1985, Negroponte was U.S. ambassador to Honduras, where he helped prosecute the contra war against Nicaragua and helped strengthen the military dictatorship in Honduras. Under the helm of General Gustavo Alvarez Martínez, Honduras's military government was both a close ally of the Reagan administration and was disappearing dozens of political opponents in classic death squad fashion. Negroponte's predecessor, Ambassador Jack Binns, had repeatedly warned Washington to take a stand to stop the killings. In one cable, Binns reported that General Alvarez was modeling his campaign against suspected subversives on Argentina's "dirty war" in the 1970s. Indeed, Argentine military advisers were in Honduras, both advising Alvarez's armed forces and assembling and training a contra army to fight in Nicaragua. President Reagan responded by removing Binns and putting in Negroponte, who, writes Eric Alterman in an MSNBC.com piece, "turned a deliberate blind eye to a murderous pattern of political killings."
On Negroponte's watch, diplomats quipped that the embassy's annual human rights reports made Honduras sound more like Norway than Argentina. Former official Rick Chidester, who served under Negroponte, says he was ordered to remove all mention of torture and executions from the draft of his 1982 report on the human rights situation in Honduras. In a 1982 letter to The Economist, Negroponte wrote that it was "simply untrue to state that death squads have made their appearance in Honduras." The Country Report on Human Rights Practices that the embassy submitted to the Senate Foreign Relations Committee took the same line, insisting that there were "no political prisoners in Honduras" and that the "Honduran government neither condones nor knowingly permits killings of a political or nonpolitical nature."
Yet, according to a four-part series in the Baltimore Sun, in 1982 alone the Honduran press ran 318 stories of murders and kidnappings by the Honduran military. In a 1995 series, Sun reporters Gary Cohn and Ginger Thompson detailed the activities of a secret CIA-trained Honduran army unit, Battalion 316, that used "shock and suffocation devices in interrogations. Prisoners often were kept naked and, when no longer useful, killed and buried in unmarked graves." In 1994, Honduras's National Commission for the Protection of Human Rights reported that it was officially admitted that 179 civilians were still missing.
During Negroponte's tenure, U.S. military aid to Honduras, a country of five million, skyrocketed from $3.9 million to $77.4 million. Much of this largesse went to assure the Honduran army's loyalty in the battle against political leftists throughout Central America. Embassy reports to Washington singled out for particular praise army chief Alvarez, a School of the Americas graduate who was direct commander of Battalion 316.
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http://www.google.com/search?q=negroponte+battalion+316&btnG=Search&hl=en&lr=