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A case presented to the U.S. Supreme Court argues Navy officials cannot discriminate against chaplains based on the denomination they represent.

The Rutherford Institute filed suit on behalf of dozens of chaplains affiliated with evangelical groups, which, according to the lawsuit, are disfavored by the Navy chaplaincy structure.

“The most fundamental guarantee of the First Amendment is that the government must remain neutral when it comes to religion,” said John W. Whitehead, president of the organization.

“As a result, religious denomination must not be a factor in the allocation of government benefits. Unfortunately, it is clear that evangelical chaplains in the Navy tend to be discriminated against when it comes to promotions and job assignments,” he said.

“It is our hope that the Navy will cease practices that clearly result in discrimination against evangelical chaplains who have answered the call to serve our country by ministering to the religious needs of servicemen and women,” said Whitehead.

The lawsuit was filed in 2001 in U.S. District Court for the District of Columbia on behalf of 34 U.S. Navy chaplains who claimed the Navy established and maintained “an unconstitutional religious quota system” that discriminated against evangelical chaplains.

Affected were their promotions, assignments and jobs, the claim said.

Rutherford in 2011 sought an injunction because of the allegedly unfair practices, but a district court and an appeals court both refused to cooperate, even though Rutherford attorneys cited statistical studies that showed “non-liturgical” chaplains were being discriminated again.

The courts ruled that the unbalanced statistics didn’t demonstrate intentional discrimination.

In its argument, Rutherford said the rulings “ignore clear precedent under the Establishment Clause holding that practices suggesting a denominational preference should be treated as presumptively unconstitutional.”

The case was filed on behalf of the Associated Gospel Churches and the Chaplaincy of Full Gospel Churches along with the chaplains.

The defendants are the Navy, Navy Secretary Ray Mabus and others.

The brief asking the Supreme Court to act noted that the Center for Naval Analysis confirmed “perceptions of bias in the promotion system are widespread” and chaplains viewed the issue as a “personal concern.”

An inspector general also concluded the Navy Chaplain Corp program had been manipulated so that “one member” anonymously can control the board results and destroy a chaplain’s career.

“Candidates whose denomination matches a board member’s have a 50 percent greater promotion probability than those with no match,” argued the brief, which pointed out that Catholic and liturgical Protestant chaplains “were the preferred denominations” while evangelicals were promoted less often.

The voting system for promotions, the brief explains, allows board members making the decision to “blackball” anyone they want by giving them a zero rating.

“No other armed service uses a ‘blackball’ procedure allowing one board member to anonymously deny a candidate promotion,” it explains.

In one example cited, under a succession of four chaplain chiefs that included three Lutherans, the proportion of Lutheran chaplains increase. But when the chiefs were Catholic, Lutheran representation dropped. Then, when a Presbyterian became chief, Catholics chaplains decreased from 21 in 2009 to six in 2013.

The brief, quoting Supreme Court precedent, said, “The clearest command of the Establishment Clause is that one religious denomination cannot be officially preferred over another.”

“The question here is will the court allow one circuit to abandon that standard, approving significant aberrations contrary to this court’s precedents?” the brief asked.

“The Bill of Rights protects individuals. The [military's] basing selection or rejection of a chaplain for promotion on denominational preferences rather than a superior record violates all rejected chaplains’ rights not to be prejudiced by the [military's] establishment of its variable ‘denominational preferences.’”

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