TEGUCIGALPA, Honduras (AP) _ U.S.-supported Nicaraguan rebels kidnapped and murdered anti-government activists on behalf of the Honduras military starting in 1980, according to Honduran sources. A rebel spokesman denied it.

Two sources close to the military commission investigating what human rights groups here say are more than 250 unresolved killings and kidnappings since 1980 said Monday that a special team of rebels performed clandestine work under orders of a Honduran counterinsurgency battalion.

A Honduran military spokesman, Col. Cesar Elvir Sierra, said he had no comment on the allegations.

Frank Arana, spokesman here for the Nicaraguan Democratic Force, the rebel group blamed for the activities, stated: ''We have participated in no such crimes in Honduras.''

Guerrillas of the Nicaraguan Democratic Force have been fighting to oust the leftist Sandinista government in Nicaragua. The Sandinistas say the rebel group is controlled by former members of the national guard of the rightist Nicaraguan President Anastasio Somoza, whom the Sandinistas overthrew in July 1979.

The Honduras Human Rights Commission says there have been 135 politically motivated killings and 138 unresolved kidnappings since the start of 1980. One source interviewed by The Associated Press was involved in part of an investigation begun by the special military commission last June, and the other has close friends in the military.

The Honduran sources, who spoke on condition of anonymity, said the main targets were Hondurans suspected of or allegedly involved in anti-government agitation and other activities. Some cases also involved Salvadorans and Nicaraguans living here, where political activity sometimes has spilled over from their neighboring countries.

They were unable to say how many actions were carried out by the Nicaraguan rebels.

The report of alleged Nicaraguan rebel involvement in human rights abuses follows a Dec. 29 communique from the military investigative commission that contained little information on the cases.

It said the commission's efforts had been hampered by a lack of witnesses and cooperation from relatives, and added that ''despite the investigations, the location of the other alleged 'disappeared' has not been determined.''

Spokesmen for the pro-American Honduran government here also have said many of the missing people are either out of the country or have secretly joined underground leftist rebel organizations.

The communique did say some of them ''could have been the victims of vendettas by irregular armed groups of the left or right, foreigners who in the past have operated clandestinely in the nation's territory.''

It also said the commission was giving itself until the end of March to finish its investigation.

The sources who provided the information said the 90-day period would give the army time to consider whether to release more of what they said was a secret, more complete account of the slain and disappeared.

They said many Honduran officers want to expose those responsible for the crimes, while others would rather put the whole affair behind them, since many of those allegedly implicated still hold high posts in the military.

The sources said the military has detailed information on the activities of a special battalion they said worked with the rebels and was responsible for many of the incidents.

According to one of the sources, a Honduran officer involved in running the battalion's operations was forced to write a detailed report on its activities after a major shakeup in the military last March.

They said Gen. Gustavo Alvarez Martinez, ousted March 31 as the military's chief, formed the specially trained intelligence battalion in 1981, originally to uncover gun-running to leftist rebels in El Salvador and Honduras from Nicaragua.

The battalion later branched into investigating internal Honduran dissidents, as well as leftist Nicaraguans and Salvadorans operating here.

The battalion was said to have been made up of intelligence specialists trained by Americans and Argentines, the sources said.

Both sources said the battalion's ''dirty war'' tactics provoked concern within the military about what Alvarez was doing to the institution's traditionally mild image and contributed to his removal last March.

''There are a lot of officers concerned about the image, as a moral thing,'' said a U.S. official, speaking on condition he not be identified. ''They want to show the current regime is different from Alvarez.''

Officials here were said to be reluctant to comment on the reports, however, because although the special battalion has reduced its activities, it is still in existence.

Among the cases cited as evidence by the sources was the September 1981 kidnapping of Virgilio Carias, a Socialist Party official, and of another man, Rogelio Martinez.

Carias told reporters that Nicaraguan captors had kidnapped the two men, beaten and interrogated them and dumped them near the Nicaraguan border.

The reports came at a time when Honduran officials seem to be taking steps to distance themselves from the Nicaraguan rebels, or ''contras,'' who have been operating at least partially from Honduran soil since 1981.