SAN SALVADOR, OCT. 9 -- El Salvador said today it would allow thousands of refugees to go ahead with plans to return from a camp in Honduras on Saturday, but would turn back American church representatives who intend to accompany them.

In a news conference, Foreign Minister Ricardo Acevedo Peralta said the group of as many as 4,500 Salvadorans from the Mesa Grande refugee camp in neighboring Honduras would be permitted to go to two government-approved relocation sites, but not to four villages that some of the refugees have identified as their homes.

The villages are in areas contested by the Salvadoran Army and guerrillas of the Marxist-led Farabundo Marti National Liberation Front (FMLN), and the government views resettlement there as part of a guerrilla plan to rebuild bases of support. A fifth village that the refugees have said they want to repopulate, Santa Marta, is among the two relocation sites acceptable to the government.

"The government will not permit the political manipulation of the refugee problem," Acevedo said, referring to the role of the foreigners accompanying the refugees. He said there was "no way" that the 10 American church activists would be allowed to accompany the refugees across the border. He accused two U.S. groups, Going Home and "Interfaith," apparently a reference to the Interfaith Office on Human Rights here, of undermining the work of a tripartite commission for refugee repatriation made up of the Honduran and Salvadoran governments and the office of the U.N. High Commissioner for Refugees.

A spokeswoman in Washington for the Religious Task Force on Central America, Margaret Swedish, said the American church activists now with the refugees in the Mesa Grande camp would try to negotiate permission to accompany them across the border Saturday without doing "anything confrontational."

In an apparent effort to put the best face on a sensitive problem, Acevedo said today that the refugees' desire to return after as much as seven years in Honduran camps shows that human rights and democracy have improved dramatically here in recent years. He said that although the government insists on orderly and gradual repatriation procedures, it would allow the Mesa Grande refugees' return in keeping with a commitment under a two-month-old regional peace plan to facilitate the voluntary "repatriation, resettlement or relocation" of refugees and displaced persons.

The government charges that rebel organizers have been active in the Honduran camps and are behind refugee demands to return en masse.

Although the refugees insist that they are acting independently out of desires to return to their home villages, there appear to be some links between the organizations supporting them and the guerrillas.

The National Committee for Repopulation, which is involved in organizing the repatriation, is an offshoot of the Christian Committee for the Displaced of El Salvador, which in turn is affiliated with the National Union of Salvadoran Workers.

Guerrilla documents captured by the military in April mention these two groups and several other organizations in terms suggesting that the rebels see them as instruments in their struggle that can be influenced to act in accordance with guerrilla plans.

The government has gone further, identifying the two groups categorically as guerrilla fronts, a charge both groups deny.

In any case, some linkage emerged publicly Sunday and Monday when demonstrators organized by the Union of Salvadoran Workers waved red flags and shouted proguerrilla slogans during peace talks between government and rebel representatives. After the talks, Salvadoran Communist Party leader Shafik Handal, one of four guerrilla commanders present, addressed the crowd and hailed the "close ties of the FMLN with the popular masses."

In a news conference Wednesday night, Duarte referred to the demonstrations and asserted that "now everyone knows that the {Union of Salvadoran Workers} and university groups are following orders from the FMLN."

Oscar Ramon Rosales Melendez, a spokesman for the National Committee for Repopulation, acknowledged that "there is a sympathy {for the FMLN} in an indirect way from some sectors" that participated in the demonstrations at the peace talks, but argued that the red flags were a "symbol of despair" for Salvadoran war dead and that proguerrilla slogans were actually shouted by military intelligence agents who infiltrated the crowd "with the aim of confusing the press."

Rosales, a former activist in the Christian Committee, was arrested in October 1985 on charges of belonging to the FMLN, he said in an interview yesterday. He was released in February in a deal in which the guerrillas freed an Air Force colonel in exchange for 57 persons on an FMLN list of political prisoners.

Rosales, who denied involvement with the rebels, said security forces have begun retaliating for the demonstrations. He said three members of a displaced-persons organization were arrested Tuesday after the rally. Terri Shaw of the Washington Post Foreign Service contributed to this report from Washington.