A federal magistrate has ruled that a series of religious services held in the Pentagon's public concourse area, violates the First Amendment's provision of the separation of church and state.

A Pentagon spokesman said yesterday that the decision by Judge Quin Elson would be studied to determine its effects on the Pentagon Pulpit Program, begun in 1942 by President Franklin D. Roosevelt.

Elson's six-page decision came in the case of an antiwar activist, John T. Shiel, 59, of 1329 N St. NW, who was arrested Nov. 23, 1977, and sentenced to spend 30 days in jail for disruption a Thanksgiving Day religious service at the Pentagon.

In his decision released this week, Elson dismissed the case against Shiel and wrote that the programs could be conducted in a room or auditorium, "as opposed to an area near commercial shops and the Metro subway." Holding the services in a public area, Elson wrote, was a violation of the constitutionally guaranteed provision separating church and state.

According to Sebastian Graber, Shiel's attorney, the Pentagon's July 4 service was held in a 300-seat auditorium, which is not located in a public area of the Denfense Department building. Graber said he was pleased by Elson's decision, which "removes the stamp of religious approval on American defense activities." Assistant U.S. Attorney John J. Klein said yesterday he has not decided whether to appeal Judge Elson's decision.

In the past guest speakers at the Pulpit Program, which a Pentagon chaplain testified was designed to appeal to "a religious majority view," have included the Rev. Billy Graham, Bishop Fulton J. Sheen and Norman Vincent Peale.

Shiel, a member of the Community for Creative Non-Violence which has staged numberous Washington protests over the proliferation of nuclear weapons, said that during the religious service he walked to the front of the audience, stood with his back to a minister who was preaching and began to address the crowd.

When Sheil refused to sit down, he was arrested and taken to Magistrate's Court in Alexandrai where he pleaded not guilty. He was found guilty and sentenced to spend 30 days of his sentence and appealed his conviction.

Last January, District Court Judge Albert V. bryan Jr. reversed Shiel's conviction and remanded the case to Judge Elson, directing him to hold hearings to determine whether Shiel's case involved First Amendment questions.