The lobbying group Citizens for Reagan has filed complaints with the Internal Revenue Service charging nine tax-exempt organizations -- including the Presbyterian Church, the American Friends Service Committee (AFSC) and the Maryknoll Fathers -- with illegal lobbying in support of the Nicaraguan government.

In a statement accompanying letters sent to the IRS this week, Citizens for Reagan charged that the groups "apparently engaged in substantial lobbying and political activities in favor of the Sandinista regime in Nicaragua and in opposition to U.S. policy in Central America."

Administration officials have said that church groups were their most difficult opponents during recent debate on President Reagan's effort to win funding for Nicaraguan rebels.

Named Thursday along with Maryknoll and the Presbyterian Church USA were the Sisters of Loretto, the National Network in Solidarity With the Nicaraguan People (NNSNP) and the Quixote Center of Hyattsville. Listed in December were the AFSC, the Central America Peace Campaign, the Community Church of New York, the Institute for Food and Development Policy and the Northern California Ecumenical Council.

Executive vice president Peter T. Flaherty asked in the complaints that the IRS investigate the groups' tax status, impose taxes and penalties, notify the groups' contributors that their donations are not tax-deductible and order the groups to stop lobbying.

"Our goal is not to get their tax status yanked, but to get the lobbying stopped, if it's illegal," Flaherty said in an interview. The complainant's statement said, "These groups are being manipulated by the Sandinistas and are participants in an extensive disinformation campaign aimed at affecting the debate in Congress."

Spokesmen for two of the groups denied illegal activity.

The Tax Code exempts church-based, charitable and educational groups from federal taxes if they do not spend a "substantial" part of their budgets in efforts to influence legislation. Court rulings have defined "substantial" to mean more than 20 percent.

"What we spend is so far under 20 percent, it's clear this is just an attempt to try to grab some headlines and tie us up in legal battles," said Debra Ruben, national coordinator of the NNSNP, a group of 60 local committees working to end U.S. involvement in Nicaragua. "We've done nothing illegal."

The NNSNP was named in the complaint along with the Roman Catholic order Sisters of Loretto, which, in a letter attached to the complaint, solicited tax-deductible contributions for the NNSNP.

Michael Lavery, assistant director of media relations for the Maryknoll Fathers, said, "It's our intent to comply with whatever the IRS code is, and we feel we have done that."

James Andrews, Stated Clerk of the Presbyterian Church USA, said from his Atlanta office that he has not seen the complaint and does not fear an investigation.

The complaint alleged that the church "has sought tax-deductible contributions to support its lobbying and political efforts" and included several publications urging readers to contact members of congress.

An IRS spokesman said tax complaints are treated as "information items that may, or may not, be investigated." The IRS routinely receives tips from the public about possible violators and, if a probe is deemed in order, the subject of the complaint is audited. "The organization or person would never know why their return is selected for an audit," he said.

Asked about the tax status of conservative lobbying groups, Flaherty said most have established tax-paying lobbying arms. "It is a touchy thing for a political organization to take on a church group," he said, "but we feel the situation has gotten to a point where we had to take action."