EL POY, EL SALVADOR, OCT. 10 -- Salvadorans who fled this country's brutal civil war began returning home today in the largest single repatriation of refugees to this country since the conflict began eight years ago.

The movement of more than 4,000 Salvadorans from the Mesa Grande refugee camp in Honduras to this border crossing quickly hit a snag when a dispute arose on the Salvadoran side over where the refugees should go first. But by late afternoon the issue appeared to have been settled, and about 1,000 of the refugees headed for their home villages in Cabanas province aboard 23 buses provided by the office of the U.N. High Commissioner for Refugees.

Others in an initial group of about 2,600 refugees went through formalities at this border post as Salvadoran troops stood by. The rest of the 4,350 Salvadorans involved in the repatriation were kept waiting at their Honduran camp and were expected to cross the border Sunday.

The repatriation plan appeared to go slowly but smoothly until a dispute developed between Salvadoran and U.N. officials and organizers of a leftist group, the National Committee for Repopulation, who were waiting for the returning refugees on the Salvadoran side of the border. The repopulation committee organizers demanded that the refugees be allowed to travel together to the capital, San Salvador, to attend a mass before going to their home villages.

After talks with U.N. officials and a delay of about an hour and a half, the committee dropped its demand to take the refugees to San Salvador.

The U.N. operations chief, Jose Maria Mendiluce, said that in a meeting last night the Salvadoran government had agreed to let the refugees go back to five villages that they fled between 1980 and 1983. Until then, the government, reluctant to take the refugees back in a large group that it views as organized by leftist supporters of Marxist rebels, had insisted on returning the refugees to two sites under firm government control.

According to U.N. officials, the five villages that the refugees want to resettle are Santa Marta in Cabanas province, Copapayo in Cuscatlan province and three locations in Chalatenango province. The government had approved the refugees' return to Santa Marta, which already has been resettled by refugees. But it had objected to the other sites, notably Copapayo, a ghost town in an area of land mines and strong rebel influence.

Col. Benjamin Canjura, the head of the 1st Military Detachment in Chalatenango province, said the Army would insist that the refugees return to their villages aboard their buses after processing and not gather for a political demonstration.

"If they go home and tend to their work, they will be fine," he said. "But if they become collaborators of the terrorists, they will have problems."

One of 10 American church activists who tried to accompany the refugees on a bus across the border from their camp in Honduras, Joseph Nangle, a Roman Catholic priest from Washington, said he and a colleague, Sister Janet Gottschalk, were told by Salvadoran officials to go back to the Honduran side of the frontier.

Nangle said that because of the history of military massacres that caused the refugees to flee, he was concerned about their safety in El Salvador. But he said it was a "consolation" that church officials on the Salvadoran side were on hand to receive the refugees.

About half of the returning Salvadorans are under 15 years of age, according to U.N. officials. Most of the others were women and older men. Few young men were visible among the poor peasants who lined up to answer a questionnaire at a row of tables staffed by 50 Salvadoran immigration officials.

Julian Portillo, a farmer from Santa Marta, said he fled with most of the village's other inhabitants in March 1981 because of military bombing. He said he still feared the Salvadoran military and was nervous about going back, but added, "we'll just have to see what happens."

Alejandra Alfaro, 11, said she was returning to Santa Marta with her mother and five brothers and sisters. "I don't remember anything about El Salvador," she said, "but I still feel I am Salvadoran."

Guillermo Cruz said he would go back to working in the fields with his machete and felt happy to be back in his homeland. Asked about the government's charges that the refugees are largely supporters of the Farabundo Marti National Liberation Front rebels, Cruz said, "We don't know anything about that."

Maria Julia Hernandez, the head of Tutela Legal, a Catholic human rights group, said the refugees were civilians and deserved protection regardless of their sympathies.

She said the repatriation was "positive," but she expressed concern about the military's view of it in light of an aerial bombing Sept. 1 near Santa Marta that left one returned refugee dead and several others wounded. She said the military claimed the victims had been mistaken for rebels.