"When allegations of abuses were brought to our attention, we in turn raised those matters with the government," said Mr. Negroponte, now ambassador to the Philippines.
He said he intervened personally to obtain the release of a young woman tortured for more than 11 weeks as a suspected subversive.
In telephone interviews and a letter faxed from Manila, Mr. Negroponte said he did not conceal human rights abuses by a military establishment vital to the Reagan administration's war against communism in Latin America.
His role and that of other U.S. officials were detailed by The Sun in a four-part June series that documented kidnapping, torture and murder by a CIA-trained Honduran military unit known as Battalion 316.
Documents declassified at The Sun's request revealed that U.S. officials knew what was happening in Honduras and engaged in a willful deception to avoid confronting Congress with the truth.
Ambassador Negroponte refused repeated requests for an interview at the time of the series, including one in a letter hand-delivered to the U.S. Embassy in Manila. He said this week that the State Department advised him not to comment.
"It was probably a mistake," he said.
The ambassador's story
Ambassador Negroponte said he wants to "set the record straight."
Mr. Negroponte said he never turned a blind eye to the Honduran military's violence, but struggled constantly behind the scenes to stop the abuses and to win the release of those he knew were held captive.
He disputed the portrait of Honduras created by The Sun's series.
"There were some serious human rights violations, [but] to say that they were systematic, numerous and that the [Honduran] government was consistently abusing the human rights of Hondurans -- I don't agree with that," Mr. Negroponte said. "There was a positive trend in the country toward democracy."
The career diplomat made these points:
* "Compared to Guatemala, El Salvador and Nicaragua, Honduras looked like a Jeffersonian democracy at that time," Mr. Negroponte said.
Hondurans enjoyed a free press, a strong labor movement and did not have the same disparities in wealth that tear apart other Latin American nations, he said. "There was not an atmosphere of repression."
* Mr. Negroponte said he intervened personally with Honduran authorities to obtain the release of Ines Murillo, a suspected subversive who was abducted and tortured for 78 days in 1983 in the secret jails of Battalion 316.
Finally, she was released alive.
* He said he never sanitized annual human rights reports sent by the U.S. Embassy in Tegucigalpa to Washington. The Sun found that those reports, prepared for Congress, played down the violence committed by Battalion 316 in order to keep U.S. aid flowing to Honduras for President Reagan's anti-Communist campaign.
"We certainly made no effort to conceal human rights abuses from Washington," he said. "We called it as we saw it."
* The ambassador stood by remarks that he made before the Senate Foreign Relations Committee in 1989, when he was asked about the activities of Battalion 316.
"I have never seen any convincing substantiation that they were involved in death squad-type activities," he told the senators.
"I stand by what I said," he said this week. "My answers are in the context of believing the country had an improving political situation and [that] the human rights violations that occurred were isolated instances and not a matter of government policy. That doesn't make them less deplorable."
Mr. Negroponte said, "I do not have any regrets about the way we carried out U.S. policies" in Central America.
"The world is not perfect. There were blemishes," he said. "But I think improvements were made.
"Over a period of time, I think the situation has improved in Central America, including in Honduras."
Mr. Negroponte's agreement to talk about events in Honduras comes as his assignment in Manila is set to end next summer. The 56-year-old ambassador has not been given a new assignment.
Thomas Hubbard, a deputy assistant secretary for Asia, has been appointed to replace him in Manila.
A vote of confidence
The State Department expressed confidence in Mr. Negroponte this week.
"Ambassador Negroponte continues to have the respect of senior members of this department. He is one of our most respected and accomplished senior diplomats, and he is doing a superb job in the Philippines," said State Department spokesman Nicholas Burns.
"I have a 35-year career and a good record," Mr. Negroponte said. "Obviously, anyone who is a public official doesn't like to have this kind of blemish. Not only because of my work in Honduras but because of my work in other posts."
But he added: "I have had four presidential appointments, three subsequent to my time in Honduras. I certainly would have no difficulty standing up in front of anybody in the Senate and explaining my role in Honduras. I think we had a positive record there."
Mr. Negroponte stressed that he achieved the main objective: to consolidate democratic rule in a country that had been governed for most of this century by military regimes. He pointed out that while he was ambassador, Honduras held its first presidential elections in nine years, and that the country has had three others since.
He said that he made reform of the Honduran judicial system a high priority. Through a judicial reform assistance program, he said, he and his staff helped Honduran courts become more independent.
"I don't believe it was a matter of government policy to violate human rights," he said, "even if there was a rogue unit under the military that in time got taken care of as well." He referred to the 1984 ouster of Gen. Gustavo Alvarez, the Honduran military chief and architect of Battalion 316.
That view differs strongly from the findings of a 1993 Honduran government report, "The Facts Speak for Themselves," in which the government acknowledged that it was responsible for the violent campaign against its own people during the 1980s.
The report lists the names of 184 people who disappeared during the decade, most of them from 1981 through 1984. Mr. Negroponte served as U.S. ambassador to Honduras from November 1981 to June 1985.
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.
"I personally made representations to secure the release of Ines Murillo," Mr. Negroponte said. "My memory is not perfect, but I remember raising it personally with the government and saying there was a concern."
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."