In their fight to pass legislation allowing military chaplains to offer sectarian prayers at public services, conservative congressional leaders have lost an erstwhile ally: the Orthodox Union.

The O.U., an organization that represents about 1,000 congregations and often joins Christian conservatives in their fight to lower the wall separating church and state, has weighed in with a letter to the ranking members of the armed services committees in the opposing the measure to permit public sectarian prayers in the military.

We “urge you to ensure that no language is included in the [Defense Department Authorization] bill which upsets the delicate balance between the core religious liberties of either chaplains or the military personnel they serve,” the O.U. wrote. “The best course of action at this stage is to defer any legislation until your committees can have full and thorough hearings on the issues.”

This past May, the House of Representatives passed an amendment to the defense bill, giving military chaplains more leeway to conduct sectarian prayers. While current law requires chaplains to pray in an inclusive manner at public occasions — for example, by omitting references to Jesus Christ — the new measure would give chaplains the “prerogative to pray according to the dictates of the chaplain’s own conscience, except as must be limited by military necessity, with any such limitation being imposed in the least restrictive manner.”

The Senate version of the defense bill passed in July did not include that change. This week, leaders of the armed services committees in both chambers are negotiating over the final bill, which is stalled as leaders in House attempt to ensure the inclusion of several controversial measures, including a federal court security bill and a controversial House anti-illegal-immigration measure.

In the past, the O.U. has taken a less public stance on religious controversies involving the military, according to Nathan Diament, director of the group’s Institute for Public Affairs. Diament said that he lobbied behind the scenes last year, when a similar measure was introduced.

This month, four Jewish groups — the American Jewish Committee, the Anti-Defamation League, the Jewish Council for Public Affairs and the Religious Action Center of Reform Judaism — joined several national Christian groups in sending a letter of opposition to all members of the House. That letter, more sharply worded than the O.U.’s, described the proposed measure as a “clear attempt to undercut” guidelines adopted by the Air Force earlier this year in the wake of a scandal over religious coercion at the United States Air Force Academy.

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