John D. Negroponte, U.S. ambassador to Honduras during the early 1980s, when the Honduran military kidnapped, tortured and murdered hundreds of people, said this week that he worked diligently behind the scenes to prevent the abuses.

"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.