The Internal Revenue Service has issued a regulation requiring certain tax-exempt church-connected institutions to file informational tax returns.

Among the institutions are some religious schools, hospitals, old-age homes and orphanages.

The new rule has been critized by the Baptist Joint Committee on Public Affairs and the leader of a coalition which has been fighting it. James E. Wood Jr., head of the Baptist joint committee, and John W. Baker, the coalition's organizer, said the regulation allows the government to define what is a legitimate activity of a church, and thus violates the First Amendment guarantee of separation of church and state.

According to the rule published Jan. 4 in the Federal Register, churches, conventions or associations of churches and an "integrated auxiliary" of a church are exempted from filing annual tax returns.

The rule defines an "integrated auxiliary" as a church organization whose "principle activity is exclusively religious," such as men's or women's groups, a seminary, a mission society or a youth organization.

The church-related hospitals, schools, orphanages and old-age homes that are being required for the first time to make extensive financial reports to the IRS will remain tax exempt, under the rule.

A religious coalition has been fighting the rule since it was proposed last February. The original languague defined integrated auxiliary" as an organization "whose primary purpose is to carry out the tenets, functions and principles of faith of the church with which it is affiliated" and whose operations "directly promote religious activity among the members of the church."

More than 80 religious groups opposed the proposal in writing and 13 of them objected to the idea at a public hearing in June. The coalition leading the struggle includes the Baptist Joint Committee on Public Affairs (which represents eight Baptist bodies), the U.S. Catholic Conference, the National Association of Evangelicals, the National Council of Churches and the Lutheran Council in the U.S.A., among others.

Baker, of the Baptist joint committee, who organized the coalition, recommended that churches "go ahead and file the returns by April 15 but under protest to show we're not sleeping on our right."

He said church leaders will appeal first to the Carter administration for a change in policy. If that fails, they will go to Congress to seek clarification of the Tax Reform Act of 1969 that prompted the IRS rule, Baker said. If necessary, some churches will take the government to court, he said.

Baker said there is no substantive difference between the original language and that of the final rule.

"We're against it mainly on principle," he explained. "The government has no business sticking its nose in and saying what a church is anyway," he said.

The 1969 Tax Reform Act said that "churches, their integrated auxiliaries and conventions of churches," which are tax exempt, are further exempted from filing the informational Form 990 return. Other tax-exempt organizations must submit the form.

An IRS spokesman said the regulation is aimed at protecting the public and is consistent with the legislative intentions of the tax act.