Nicaraguan troops have removed thousands of Miskito Indians from their villages along the Honduran border in the remote Atlantic Coast area as part of what officials described as the largest military operation since the 1979 revolution.

The officials said the government began the evacuations around Jan. 1 after 26 persons, most of them Sandinista soldiers, were killed and another 22 abducted in a series of incursions by guerrilla bands made up of Miskitos and former members of the Nicaraguan National Guard operating out of Honduras.

The evacuations follow a history of deep antagonism between the Sandinista leadership and the Miskitos, who traditionally have lived in isolation from whatever government was in place in Managua. Attempts to impose central authority after the Sandinistas took control of Nicaragua in July 1979 were met with Indian displeasure.

That displeasure turned into hostility as the Sandinistas began to upgrade the military presence in the region, augmenting their own forces with Cuban doctors, teachers and soldiers who, the Indians charged, were interfering with Indian culture and local power structures.

Following a complete break with Indian leaders early last year, and the fleeing of a number of Miskitos over the border, the Sandinistas increasingly have tied the Indians in Honduras to anti-Sandinista activities of exiled soldiers of the government of Anastasio Somoza, which was overthrown in 1979.

The government justified the evacuations as necessary to protect loyal Indians and to thwart a plan to create a "theater of operations for counterrevolutionary actions."

Vice Interior Minister Rene Rivas charged in an interview that Somoza's National Guardsmen were working with a Miskito leader, Steadman Fagoth, and several leaders of the fundamentalist Moravian Church to foment an uprising by the Miskitos. He said their goal was to declare the region independent.

About 20 villages that once held about 10,000 people were emptied. Rivas said the villagers cooperated and that there were no injuries. He said that an undetermined number of Miskitos crossed the Coco River that forms the border with Honduras before troops could evacuate them.

Since the government has turned down reporters' requests to travel there, it was impossible to verify the official account. One independent traveler to the region during the first two weeks in January, however, said that he had seen as many as 80 Army trucks full of Indians, and that prisoners were being held in Puerto Cabezas' only high school.

Rivas acknowledged that the Sandinista police were holding "more than 40" prisoners in the school.

The traveler also said people in the area said the Indians were being taken to settlements near the isolated mining town of Siuna.

The military action in the area, which involved reclaiming two towns occupied by Somoza supporters and Miskito forces and raiding a training camp, involved "no more than 2,000 troops," Rivas said.

The isolated province of Zelaya has been the subject of intense rumors for weeks in Managua since the government imposed a news blackout on the area and began limiting foreigners' travel there.

It has also become a central issue in the strained relationship between Nicaragua and the United States. Last week, the State Department warned American citizens of the restrictions on travel in Nicaragua. "As a point of explanation," the advisory said, the restrictions followed a number of other actions against the Miskitos and religious workers. It noted without explanation that "there are also numerous though unconfirmed reports of repressive tactics by government forces."

A response issued by the Nicaraguan Embassy in Washington called the advisory "an unheard-of departure from the norms of proper international conduct" that contained "patently false accusations" made to discredit Nicaragua and prepare U.S. opinion for actions against its government.

Nicaragua has charged that the Honduran-based anti-Sandinista guerrillas operate in conjunction with exile groups training commandos in southern Florida and California. The Sandinistas have asked for a U.S. investigation into possible violations of American neutrality laws.

Although the exiles have publicly acknowledged their activities and intent to overthrow the Nicaraguan government, the United States has declined to investigate their U.S. actions on the ground that are doing nothing illegal. Government spokesmen have said that the law covers only actual military actions against a friendly country launched from U.S. soil, and that they have no evidence of this.

The northeastern part of Nicaragua is radically different in culture and language from the populous Pacific Coast. Besides the Indians, many of the inhabitants are English-speaking blacks. The approximately 100,000 members of the Miskito community speak their own language and view those from the west coast with suspicion.

The east coast is inaccessible by road and is a pocket of deeper poverty and underdevelopment than the Spanish-speaking west.

During an interview in his office, Rivas showed video cassettes of Miskito prisoners telling about their involvement in organizing the planned insurrection and receiving training in weapons from former National Guardsmen in a camp near the coastal town of Sandy Bay.

One of the prisoners, staring straight ahead and speaking in halting Spanish, said he had taken part in an attack Dec. 18 on the village of San Carlos and that he had watched while his comrades drove a stake into the throat of a wounded soldier and mutilated the genitals of another.

Another prisoner, who looked relaxed, and appeared to speak spontaneously, said he was a Moravian clergyman named Maurice Vidaure. He said he helped the insurgents by providing money and supplies through the church's social-action committee.

A girl shown on the tape said she had been in a Sandy Bay training camp, where she said the leaders had the young recruits sing religious songs on arrival and promised guns and training.

Rivas named 10 Moravian clergymen he said were prisoners or wanted by the police in connection with the insurgency. He said, "The Moravian church, as a church, was involved in the counterrevolutionary action. The pastors persuaded the young people to go over into the camps, preaching a primitive brand of anticommunism."

He said, however, that no members of the Moravian Church hierarchy were suspected.

In anticipation of probable criticism of the displacement of the Miskitos, Leonte Herdocia, the head of the Nicaraguan National Commission for Protection and Promotion of Human Rights, a government-appointed body, said international observers would be invited to visit the area as observers.

Rivas traced the trouble with the Miskitos to the falling out early last year between the Sandinistas and Fagoth, the leader of the Miskito organization called Misurasata. Fagoth originally supported the Sandinista government, he said, and was named a member of the state council.

But the Sandinistas expelled Fagoth from the council last February and jailed him, charging that Somoza government files showed that he had offered to work as an informant for Somoza's security police. Several other Miskito leaders also were arrested at the time, Rivas said, and the arrests "were taken as hostility toward the Miskito people."

He said Fagoth was released several weeks later, and began to encourage Miskito young people to follow him into Honduras.

He said the camps in Honduras and the Sandy Bay camp were eventually joined by Somoza guardsmen who had been fighting sporadically against the Sandinistas since the 1979 victory from sanctuaries in western Honduras.

Attacks across the Coco River began in late November, Rivas said, adding that there were 11 incidents between Nov. 22 and Jan. 2. Twenty-six soldiers and four civilians were killed and 22 persons abducted, according to Interior Ministry reports cited by Rivas.

All of the attacks occurred along the approximately 100-mile stretch of river between Waspam and the village of Raiti, in an area so remote that the only means of transport is by river boat.

In two attacks, according to Rivas, in the towns of San Carlos, just east of Raiti, and Bilwascarma, near Waspam, townspeople welcomed the attackers and rang churchbells in celebration.

On Dec. 28, the government counterattacked. The Sandy Bay training camp was attacked with troops in a helicopter and two transport planes, and 30 guerrillas escaped, Rivas said.

Then, in what he said was perhaps the government's most important decision to date, Managua ordered the evacuation of the villages west of Waspam on the river, he said, "to guarantee their food supply and protect them from the fighting."