Another story in September about dozens of children protesting the disappearances outside the Honduran Congress as it considered forming a committee to investigate military abuses.
"There is no way United States officials in Honduras during the early 1980s can deny they knew about the disappearances," said Jaime Rosenthal, a former vice president of Honduras and owner of the daily newspaper El Tiempo. "There were stories about it in our newspaper and most other newspapers almost every day."
"[The United States] had an embassy staff here that was larger than most other embassies in Latin America," Rosenthal said. "If they say they did not know, that is bad, because it would mean they were incompetent."
Evidence came from other sources.
Efrain Diaz Arrivillaga, then a delegate in the Honduran Congress and a voice of dissent in the prevailing atmosphere of intimidation, said he spoke several times to Negroponte about the military's human rights abuses.
Diaz said that in meetings at the U.S. Embassy and at social occasions, he rebuked Negroponte for the U.S. government's refusal to take a stand against the repression.
The Honduran legislator said Negroponte reproached him for refusing to take a strong stand against Communists who were trying to seize control of Honduras.
"I remember Negroponte told me, 'You and others, what you are proposing is to let communism take over this country and over the region,' " Diaz said.
"The most important thing to him was to win public support for the presence of the U.S. military in Honduras," Diaz said. "Their [the U.S.] attitude was one of tolerance and silence. They needed Honduras to loan its territory more than they were concerned about innocent people being killed."
Accusations against the military also came from former insiders.
In August 1982, Col. Leonidas Torres Arias, ousted chief of intelligence for the Honduran military, issued a public warning about Battalion 316. In a news conference in Mexico City, he told reporters about "a death squad operating in Honduras led by armed forces chief General Gustavo Alvarez."
The story made headlines in Mexico and across Central America. reporter from the Honduran newspaper El Tiempo asked Negroponte about the colonel's allegations.
Said Negroponte in an article that appeared Oct. 16, 1982: "Democracy is being consolidated in this country. The armed forces have supported that process. It was the armed forces that turned over power to the civilian constitutional leaders of Honduras. So, I have a lot of difficulty taking those kinds of accusations seriously."
The evidence was also to be found in the streets of Tegucigalpa.
Each week, hundreds marched through the streets of the capital demanding the release of the disappeared. Sometimes they marched past the U.S. Embassy, a hulking concrete complex on Paz Avenue.
The Committee of the Relatives of the Disappeared in Honduras (COFADEH) turned to the U.S. government for help. On June 13, 1983, COFADEH addressed an open letter to Richard Stone, President Reagan's special envoy to Central America, complaining that the Honduran military was holding dissidents in clandestine jails.
"More than 40 people have been illegally arrested and tortured," the letter said. "Some have never been heard from since their arrest."
The letter was published in El Tiempo, one of the largest newspapers in Honduras. The U.S. government never responded to the committee's pleas.
In an interview, Stone said that he did not recall the letter.
In October 1983, members of COFADEH visited the U.S. Embassy to ask for help. They said they met with Scott Thayer, a junior political officer assigned to monitor human rights. Among the relatives who attended was Bertha Oliva, whose husband, Tomas Nativi, had been missing for more than two years.
Also there was Zenaida Velasquez, whose brother, Manfredo, had been missing for more than two years.
The parents of Eduardo Lanza attended. Lanza, a medical student, had been a prominent student leader when he was kidnapped by Battalion 316 in August 1982.
The group told Thayer that they had searched jails and hospitals across Honduras for their missing relatives, that military officials only laughed at them and that judges were too afraid to help. They begged the embassy to use its influence with Honduran officials to win their relatives' freedom.
Zenaida Velasquez remembers that Thayer listened politely, then dismissed their allegations.
"He said he knew Honduras had a democratic government and [that] those kinds of practices were not going on," Velasquez said. "They were such a bunch of liars it was disgusting."
Thayer, now a political officer at the U.S. Embassy in Madrid, Spain, said that meeting with Hondurans about human rights abuses "was part of my job. I recall having meetings like that, but I can't recall that specific meeting."
Oliva still fumes over the meeting. In an interview in Tegucigalpa, she said that the embassy official acted as if they were fabricating the disappearances of their relatives.
"He was very cold, very cold," she said, pursing her lips. "Any kindness was gone. He did not even smile at us."
Roberto Becerra, father of the student Eduardo Lanza, said he came away from the meeting with a hopeless feeling.
"We felt like we were screaming in the desert. No one heard us. No one would help us."
In at least one case, Negroponte was confronted with evidence of abuse that he could not ignore -- the arrest and torture in July 1982 of journalist Oscar Reyes and his wife, Gloria.
Reyes, a founder of the journalism school at the National Autonomous University of Honduras, was openly sympathetic to the Marxist Sandinistas in Nicaragua and had written numerous newspaper columns criticizing the Honduran military.
The abduction of the Reyeses sparked newspaper stories and raucous student protests. The Reyeses said they were locked in secret cell for a week, and beaten and tortured with electric shocks.
At the U.S. Embassy, there was fear that if the story got to the United States it might damage carefully assembled public support for the Central America program operating out of Honduras.
Cresencio S. Arcos, then the embassy press spokesman, alerted Negroponte that the Honduran military had abducted the Reyeses.
"If they do this guy, then we're in trouble," Arcos warned. "We cannot let this guy get hurt. ... It would be a disaster for our policy.
"The ambassador did approach [General] Alvarez about this to manifest his concern," Arcos said.
The case clearly shows that Negroponte knew of the Reyeses' abduction and that the ambassador acted in such cases when he felt compelled to do so.
Reyes and his wife were released from the clandestine jail after a week. They were taken before a public court and sentenced to six months in prison. Two weeks before their sentences ended, they were allowed to leave for the United States on condition that they keep quiet about the torture they endured.
That condition was laid down personally by Alvarez, said the Reyeses, who now live in Vienna, Va.
The U.S. Embassy also kept quiet publicly about the Reyes case. It was not mentioned in the human rights report for 1982, even though it was widely covered in the Honduran press and illustrated the Honduran military's violation of human rights on several counts: illegal abduction, secret incarceration, torture and suppression of press freedom.
Instead, the 1982 report asserted: "No incident of official interference with the media has been recorded for several years."
Negroponte's aides at the embassy told The Sun that they knew about serious human rights abuses by the Honduran military, and that the violence was a subject of constant discussion.
One of those aides was a junior political officer, Rick Chidester, who was assigned in 1982 to gather information for the embassy's annual report on human rights, a task that usually fell to a junior officer.
Chidester, now 43 and a private businessman, said that while in Honduras, he interviewed human rights advocates and journalists who provided him with information that the Honduran military was illegally detaining, torturing and executing people.
"I had allegations about vans coming up to police cells and taking out people they [the Honduran military] didn't want ... and shooting them," Chidester said. "I had allegations that, as part of the interrogation techniques, torture was being used."
He said he included the allegations in his draft of the 1982 report.
A supervisor, who Chidester will not name, demanded proof -- sworn testimony or photographs of torture victims. Chidester said he was admonished for basing his report on rumors when he was unable to produce such evidence.
Chidester said he argued that while he had not interviewed torture victims, the allegations came from too many credible sources to be ignored, and that the reports were not supposed to be limited to provable facts.
"While the State Department is not an investigative body, we're supposed to analyze political events and identify trends," Chidester said. "Our analysis is valuable, even if based on opinion and not admissible as proof in a court of law."
His arguments failed.
By the time the report reached the U.S. Congress, the serious accusations against the Honduran military had been removed. Allegations that remained were described as unsubstantiated or isolated abuses that had been dealt with swiftly by the Honduran government.
Overall, the report portrayed Honduras as an emerging democracy where the civilian government and military respected human rights.
The report was such a misrepresentation of the facts that Chidester recalls joking with others in the embassy: "What is this, the human rights report for Norway?"
While Negroponte has refused to be interviewed by The Sun, his boss at the time of his appointment to Honduras described the priorities on human rights.
Thomas Enders, the assistant secretary of state who told Negroponte's predecessor to stop reporting rights violations through normal channels, said it was crucial to keep U.S. aid flowing to Honduras.
"What we were attempting to do was, on the one hand, to maintain our ability to act in Central America. That is, our congressional authority to send economic and military aid, so we avoided direct public confrontations against the military in El Salvador and Honduras," he said.
"And at the same time, privately we were spending an enormous amount of effort in order to change the way they looked at how they behaved. There was endless jawboning."
Instead of telling Congress what was going on in Central America, the Reagan administration employed the State Department human rights reports as instruments to advance policy objectives.
Consequently, the human rights reports differed sharply in tone, depending on whether the government was a friend or foe.
The 1982 report on Nicaragua -- where the United States was trying to topple the Marxist Sandinista regime -- made strong charges against that government.
A section titled "Respect for the Integrity of the Person, Including Freedom from Killing" said: "There is credible evidence that security forces have been responsible for the death of a number of detained persons in 1982."
In the same section of the Honduras report for 1982, the State Department said: "Allegations that death squads have made their appearance in Honduras have not been substantiated."
Cresencio Arcos, press spokes-man in the U.S. Embassy in Tegucigalpa from June 1980 to July 1985 and U.S. ambassador from December 1989 to July 1993, explained the difference:
"Invariably, the result in this process was to magnify your enemies' misdeeds and minimize your friends' misdeeds," he said.
Ambassador Negroponte also made numerous public statements praising the Honduran military for supporting the civilian government and for respecting the rights of its people.
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."
In October 1982, he wrote to The Economist: "Honduras' increasingly professional armed forces are fully supportive of this country's constitutional system."
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.