In a ruling that could cost Christian Science health care providers millions of dollars, a Federal judge has declared that Medicare and Medicaid reimbursements to the faith's nursing centers violate the constitutional separation of church and state.

The decision, handed down on Wednesday by Judge Richard Kyle of Federal District Court in St. Paul, held that the Government had ''gone too far'' in trying to accommodate one group's religious beliefs by including 15 provisions within Federal Medicare and Medicaid laws that specifically mentioned Christian Science, in order to allow reimbursements to the faith's institutions.

The decision will be appealed, a spokesman for the nursing centers said.

Founded by Mary Baker Eddy in Boston in 1879, the First Church of Christ, Scientist, teaches that illness results from false thinking and should be treated spiritually. Nationwide, Christian Scientists operate 23 nonprofit nursing centers that treat disease and injury through prayer rather than medicine or surgery.

The centers are independent of the Mother Church in Boston, said a spokesman, W. Michael Born. Collectively, they receive about $7.5 million a year in Medicare reimbursements, which have covered patients' room and board, supplies and basic nursing services, Mr. Born said. He said the payments did not cover the services of Christian Science practitioners, who are trained to pray for patients' healing.

Judge Kyle granted an immediate stay of the decision, in the expectation of an appeal.

A spokesman for the Department of Health and Human Services said the department would have no comment until it had seen the ruling.

The suit, filed by Robert J. Bruno, a Burnsville, Minn., lawyer, named as defendants the Federal Department of Health and Human Services and the Health Care Financing Administration. The judge allowed the First Church of Christ, Scientist, to join the suit as a defendant.

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