Mr. Negroponte said that when he learned of rights abuses, he expressed concern to Honduran government officials, including Honduran President Roberto Suazo Cordoba, Foreign Minister Edgardo Paz Barnica and General Alvarez.
The most notorious case was that of Ines Murillo, who was abducted as a suspected leftist at the age of 24 in 1983. For 78 days, Ms. Murillo was subjected to tortures that included being hung naked, nearly drowned and shocked with wires attached to her breasts and genitals.
Mr. Negroponte said that when he spoke about such violence with General Alvarez, the Honduran would deny that abuses were being committed.
Asked whether he believed the general's denials, Mr. Negroponte said: "Not entirely, no."
"Alvarez was different from many of his colleagues in the Honduran military," Mr. Negroponte said. "Whether he believed in death squad activity, I really don't know that."
Mr. Negroponte said he did not believe U.S. officials could be held responsible for "individual abuses by Hondurans against Hondurans."
"That's the responsibility of those Hondurans who committed the violations, and if they can still be punished under Honduran law, that's what should happen to them," he said.
In his letter to The Sun, Mr. Negroponte defended the truth of annual human rights reports on Honduras.
"The annual human rights reports prepared by the Department of State during my tenure dealt candidly with issues concerning the respect for the integrity of the person, including such problems as alleged disappearances, torture, arbitrary arrests and other human rights violations," he wrote. "There was no effort to soft pedal these matters."
Rick Chidester, formerly a junior political officer in the U.S. Embassy in Honduras, spoke with The Sun about how the human rights report for 1982 was sanitized. Mr. Chidester, who was assigned to write the first draft, said he compiled substantial evidence of abuses by the Honduran military but was ordered to delete most of the accusations from the report.
"Not by the ambassador," Mr. Negroponte insisted this week.
"I'm not trying to say we had no responsibility for them whatsoever," he said. But he added that the annual human rights reports are touched by many hands, beginning with an embassy's political section, before they are "sent to Washington, edited, redrafted, retransmitted."
As for the embassy's role, he said, "You know the process. I don't personally draft them because we want the staff to call it the way they see it."