In a letter to the New York Times, published on Sept. 12, 1982, he wrote: "Honduras' increasingly professional armed forces are dedicated to defending the sovereignty and territorial integrity of the country, and they are publicly committed to civilian constitutional rule."
That was the same year journalist Oscar Reyes and his wife were abducted and tortured by the Honduran military for a week because of articles he had written.
On Aug. 12, 1983, the Los Angeles Times published a Negroponte column in which he acknowledged that there were credible allegations of some disappearances."
However, he added: "There is no indication that the infrequent human rights violations that do occur are part of deliberate government policy. Indeed, disciplinary action has been taken against members of the police and military (including officers) who have abused their authority."
That year, in a case that gained notoriety, the 24-year-old leftist Ines Consuelo Murillo was held for more than 11 weeks -- naked, beaten, suffocated, shocked, fondled and threatened with rape.
To this day, none of her torturers has been punished.
Arcos said that Negroponte privately expressed concerns about abuses to Honduran officials.
"The ambassador did pressure the Hondurans. Not publicly. Quietly," Arcos said.
"We were concerned by the issue. Reports [of human rights abuses] were increasing."
Even years after he left Honduras, Negroponte would not publicly acknowledge the crimes of kidnapping, torture and murder that were committed by the Honduran military.
During his Senate Foreign Relations Committee confirmation hearing as ambassador to Mexico in 1989, Negroponte was asked about Battalion 316 and its abuses.
"I have never seen any convincing substantiation that they were involved in death squad-type activities," he said.