Soon there may only be atheists in the foxholes.

Christians are leaving the U.S. military or are discouraged from joining in the first place because of a “hostile work environment” that doesn’t let them express their beliefs openly, religious freedom advocates say.

Michael Berry, senior counsel at the Liberty Institute, a Texas-based legal organization dedicated to defending religious liberty in America, said recent high-profile cases of military chaplains facing punishment for private counseling sessions that reflected the teachings of their religion could cause devout Americans who are qualified for military service to think twice about joining the military.

In December, a chaplain for a Ranger training battalion received an administrative letter of concern after a soldier complained that he advocated Christianity and used the Bible during a mandatory unit suicide-prevention training session. The Military Association of Atheists and Freethinkers said the chaplain “used his official position to force his personal religious beliefs on a captive military audience” in an article the group posted on its website.

And, last month, a Navy chaplain was removed from his post and may lose his career after some sailors complained about his private counseling, in which he reportedly advocated against homosexuality and sex outside of marriage.

Mr. Berry represents both chaplains in question.

“People of faith are going to stay away from the military,” said Mr. Berry in an interview with The Washington Times.

“I can’t tell you how many moms and dads I’ve spoken to who say, ‘My son or daughter wants to join the military, [but] in light of what you’ve described, I’m not sure I want to let them join the military anymore,’ and I don’t blame them. I would have serious reservations about my own kids joining,” Mr. Berry said.

Douglas Lee, president of the Chaplain Alliance for Religious Liberty, whose job it is to find people who want to be chaplains and make sure they’re also qualified to serve in the military, said growing religious hostility within the military is making it harder for him to find potential recruits and for the armed forces to maintain the chaplains it does have.

“I know people who get out, officers and chaplains, who’ve said, ‘I can’t serve the way I want to in this environment,’” said Mr. Lee, who also served as an Army chaplain. “People who’ve said, ‘Because of the religious liberty challenges I see, I think I’ll serve somewhere else.’”

Not being able to recruit or retain these individuals is very dangerous from a national security standpoint, said Mr. Berry, because they could be the military’s next group of leaders, but will never serve because they don’t think they’re welcome.

“We all used to sit around and talk about planning on spending 20 years, but at some point enough is enough,” he said.

Mr. Berry said he thinks the “hostile work environment” that is forcing the most religious persons out of the military is only getting worse, and that while in the past problems were mainly in the Air Force, religious liberty issues have spread throughout all the services.

“The problem is getting worse, not better, despite our efforts,” he said. “There is a culture [of] hostility [toward] religion in the military right now.”

While problems in the past have touched all religious groups, Travis Weber, director of the Center for Religious Liberty at the Family Research Council, said he’s seen a recent uptick and pattern of Christians facing persecution for religious expression.

Mr. Lee blamed a lack of education among commanders about where the line is to express religion in the workplace that causes a knee-jerk reaction to any show of religion.

A commander recently told a gate guard on a base in Georgia that he could no longer tell someone to have a “blessed day,” for example, though further review found that wasn’t a religious imposition, he said.

In the chaplain example last month, Navy Chaplain Lt. Cmdr. Wes Modder was removed from his position counseling sailors and could be kicked out of the military for expressing his views on marriage and homosexuality in private sessions. Mr. Berry is representing Lt. Cmdr. Modder, who is still on active duty in Charleston, South Carolina, as the case is reviewed at a higher level.

Mr. Berry said this case even could set a precedent usable outside the military by establishing, as a principle, that the government can punish religious leaders based on the state’s moral disapproval of the church’s teachings, especially in matters of sex.

“If what happened to Chaplain Modder is allowed to stand, it could foretell more instances in which the government tells priests, ministers, chaplains, etc. that their views are unacceptable,” he said.

Mr. Weber said these types of punishments affect both troops and chaplains, since chaplains will feel the need to constantly be looking over their shoulder to avoid punishment, and service members will wonder if chaplains are being honest or just saying what they can say without getting in trouble.

Michael Weinstein, president of the Military Religious Freedom Foundation, said that while chaplains can believe whatever their religion teaches, those who think they must act on religious teachings about sex or sexuality have no place in the military.

“You can continue to believe that internally, but if you have to act on that, the right thing to do is to get out of the U.S. military, because you have no right to tell a member of the military that they’re inferior because of the way they were born,” he said.

The military had 2,837 active-duty chaplains as of December 2014, according to numbers provided by the Defense Department. The largest group was the Southern Baptist Convention, with 437 members. More than 200 chaplains are affiliated with the Roman Catholic church, while 26 are Jewish, and just one is Hindu.

“The Department of Defense respects, places a high value on and supports by policy the rights of members of the military services to observe the tenets of their respective religions or to have no religious beliefs,” said Lt. Cmdr. Nate Christensen, spokesman for the Defense Department. “The mission of the chaplain corps is to provide care and the opportunity for service members, their families and other authorized personnel to exercise their constitutional right to the free exercise of religion.”

Advocates agreed that chaplains play a crucial role in allowing troops to exercise their freedom of religion, no matter what religion that is.

Commanders have also relied on chaplains to act as combat multipliers, dealing with issues in the ranks like marriage crises or financial troubles that commanders often can’t address, Mr. Lee said.

Mr. Weinstein, however, said he thinks the chaplain corps would work better if chaplains were totally outside the military force structure and didn’t have a military rank.

In addition to posing a problem if a chaplain outranks whoever is seeking counseling, having religious leaders in the military serves as propaganda for Islamic extremist groups, who try to paint the U.S. military as the latest group of religious crusaders, he said.

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