Churches in cities throughout the United States have begun to revive the ancient rite of sanctuary in an unprecedented effort to protect victims of political turmoil in Central America.

Defying the Immigration and Naturalization Service, a church in Racine, Wis., has harbored 12 illegal refugees from El Salvador and one from Guatemala for the last two weeks.

Two illegal immigrant women, one of whom says she was raped by soldiers in El Salvador, have lived in a Seattle church for the last week, and churches in Chicago, Tucson, Los Angeles, Boston and several other cities have set up sanctuaries or announced such plans.

The rite of church sanctuary has no standing in modern American law, but it has proved to be an effective barrier to INS agents. They have been barred by their rules and a fear of adverse publicity from entering religious institutions to arrest illegal aliens.

No government agents have attempted to challenge the sanctuary movement, and INS spokesman Duke Austin said today in Washington that the agency has no plans to drop its longstanding policy "not to go into churches, neighborhoods or homes to make arrests of illegal aliens" or of those harboring them.

But he said INS reserves the right to do so if it sees such searches as necessary. The agency can make such arrests and can, with a valid search warrant, enter churches, he said.

Several ministers in the sanctuary movement said they want INS and the State Department to give the Central Americans the same protection granted Cuban and Polish immigrants, not reject them as "economic refugees" merely seeking better jobs and living conditions in the United States.

Illegal aliens may apply for political asylum in the United States if they can prove that they would be subject to persecution if they returned home.

Sanctuary, said the Rev. Philip Zwerling, senior minister of the First Unitarian church here, "has a long tradition, dating back to Exodus and to medieval canon law. If you offended the king and were in fear of your life, you could seek refuge in the church."

Zwerling's congregation voted, 81 to 0, last weekend to use a former Sunday school room as housing for Central American refugees needing protection.

The Rev. Donovan Cook, senior minister at University Baptist Church in Seattle, said members of his congregation realize they are violating the law but are willing to take the risk after hearing "horrifying stories" from Central American refugees.

One of the illegal immigrant women in his church said she was arrested in El Salvador with her 6-year-old child after being active in Roman Catholic efforts to help the poor. Cook said she told church members "she had been beaten, raped and tortured in front of the 6-year-old."

Private organizations working with refugees estimate that as many as 250,000 Salvadorans may be living illegally in this country. Efforts by churches to help them began more than a year ago and at first focused on the South Side Presbyterian Church in Tucson.

But the movement did not spread to many other congregations until late last year. Jim Corbett, a retired Tucson rancher who has helped many illegal aliens from Central America escape U.S. authorities, said hundreds have used the Tucson church.

As many as 20 have stayed there at one time, he said, before moving on to Los Angeles, Chicago or other cities where they have friends or relatives.

Lee Holstein, coordinator of the Chicago Religious Task Force on Central America, said illegal aliens have taken refuge in churches in Tucson; Chicago; Berkeley, Calif.; Milwaukee; Racine; Seattle, and Wayzata, Minn. In addition, churches have announced themselves ready to take in illegal aliens in Washington; Boston; Lawrence, N.Y.; Southampton, Pa.; Colorado Springs; Madison, Wis., and Los Angeles, she said.

"Since October, the response has been incredible," Holstein said. She estimated that 20,000 people have been involved in helping illegals escape detection.

Holstein said interest in the program has grown so rapidly that she expects the number of churches offering sanctuary to double in two or three months.

A booklet prepared by Holstein's organization warns interested individuals and churches that they are liable to arrest under federal law for harboring undocumented aliens. The maximum penalty, Holstein said, is a $2,000 fine and five years in prison for every illegal alien assisted.

Cook said refugees fear applying for asylum because they think that their names will then be leaked to their home governments and that their relatives will suffer.

Paula Kuzmich of the State Department's Bureau of Human Rights and Humanitarian Affairs said that applications are kept confidential and that she knows of no leaks that had caused any suffering.

Cook said, however, "We just don't trust the State Department."