A Honduran Army allegation that CIA-trained Nicaraguan rebels were involved in political killings and kidnappings here comes during a period of new scrutiny of the so-called ``secret war'' against Nicaragua. The Honduran military has become increasingly alarmed by the possibility that Honduras could become the sanctuary for thousands of well-armed, unemployed guerrillas if Congress blocks the Reagan administration's request for renewed aid this year to the contra rebels who are fighting the Nicaraguan government.
The military leadership's unease with the contra presence coincides with a need to explain the results of an in-house armed forces investigation into more than 247 kidnappings and killings here since 1980.
The allegation that more than 18 Hondurans and an unknown number of Salvadoreans and Nicaraguans were killed or kidnapped by the rebels was leaked to reporters earlier this month by top Army officers on the heels of a military report blaming foreigners for much of the political violence.
The senior officers, who declined to be identified, also blamed Salvadorean rightist and leftist groups for some of the killings or disappearances of more than 60 Salvadoreans here during the period probed.
The official Army commission still investigating the violence has declined to say what, if any action they will take against members of their own security forces found to be responsible for abuses.
Human rights figures here first dismissed the reports of foreign involvement as an attempt to ``whitewash'' official abuses.
However, Ramon Custodio, the head of the watchdog Honduran Human Rights Commission, says he is now investigating the possibility that the contras are to blame for some of the violence in this country.
``We have found direct and indirect evidence that the contras were responsible for some of the human rights violations that we have denounced,'' said Mr. Custodio, who claims that a Nicaraguan rebel officer recently threatened him and accused him of being a ``communist.''
``But the [Honduran] Army had to have had knowledge of this and been in official compliance,'' he said, echoing a common charge among opposition figures.
Top Honduran officers said many of the contras' victims were suspected of being involved in arms traffic to the Salvadorean guerrillas.
``They [contras ] would pick them [Salvador rebels] up, question them, and sometimes torture and kill them,'' said one officer.
President Reagan said that arms interdiction was one of the major aims of the ``covert war'' when he approved $19 million in funding for the contras in 1981.
At the same time, a special Honduran armed forces crack intelligence squad, the division of special investigations, was created to crush clandestine support networks for Honduran and Salvadorean leftist movements.
The division, charged with involvement in kidnappings and disappearances by human rights groups, was said to have worked closely with counter-intelligence operatives of the Nicaraguan Democratic Force (FDN), the largest rebel group here.
The unit's leadership was dissolved by armed forces chief Brig. Gen. Walter L'opez Reyes after he took power in a March 31 barracks coup for reasons that were as political as they were humanitarian.
General L'opez worried that the division, which came under the direct comand of ousted Army chief Gen. Gustavo Adolfo Alvarez Mart'inez, could serve as an intelligence network hostile to consolidation of his power.
For the same reason, he distrusted contra leaders linked to the squad.
Choluteca, a province strategically situated between El Salvador and Nicaragua, was the site of arms increased interdiction activity by both contras and security forces in 1982 and 1983, when a simultaneous crack-down on opposition figures ocurred, residents say.
Raul Sandoval, a union activist forced to move to Tegucigalpa during that period, said that in late 1981, members of a group called the Honduran Anti-Communist Movement, (MACHO), began threatening local opposition figures.
``Choluteca was filled with contras then,'' he said. ``They threatened us and accused us of being communists or Sandinista spies.''
In June of 1982, union activist Saul Godinez was abducted by Nicaraguan rebels on his way to work just outside of the town of Choluteca, Mr. Sandoval said. He was never seen by his wife and family again.
In most cases, however, the lack of witnesses or hard evidence makes it hard to pin the blame on the rebels.
In April of 1983, unknown gunmen dumped the body of schoolteacher Cesar Augusto Cadalso Davila on the side of a highway near the Choluteca province town of El Triunfo.
The Human Rights Commission blames the contras for the killing since Mr. Cadalso said he had received several threats on his life from contras and had moved from El Triunfo several months earlier when unknown gunmen sprayed his house with automatic weapons fire.
But Cadalso also complained to his friends that local security forces sometimes arrived with the contras, leaving it unclear who is responsible for his death.
Adolfo Calero, head of the FDN, said he had ``no knowledge'' of any such abuses and called the charge ``an internal Honduran matter.''
Most residents say that contra intimidation dropped considerably after Alvarez was ousted, but there is still fear in border towns like San Marcos de Colon, where the rights commission says contras killed to two Honduran peasants in December.
``It is very dangerous to speak out against the contras,'' says one resident. ``It is better to keep your mouth shut.''
In 1982, teachers in the Mosquitia border region went on strike for four months after receiving threats from Miskito Indian guerrillas who accused them of spying for Sandinista troops. But their plea for official protection was ignored by the armed forces, who were apparently annoyed that the teachers had denounced the ``secret'' presence of the contras.