Thousands of Americans, including former Arkansas Gov. Mike Huckabee and famed evangelist Franklin Graham, have come to the defense of a chaplain who could be thrown out of the Navy because of his Christian faith.

Michael Berry, an attorney at Liberty Institute, a law firm that specializes in religious liberty cases, told me his client categorically denies making any such statements. He said the chaplain is the victim of a setup.

Lt. Cmdr. Wes Modder has been accused of failing to show “tolerance and respect” in private counseling sessions regarding issues pertaining to faith, marriage and sexuality – specifically homosexuality.

Michael Berry, an attorney at Liberty Institute, a law firm that specializes in religious liberty cases, told me his client categorically denies making any such statements. He said the chaplain is the victim of a setup.

Modder, who is endorsed by the Assemblies of God, has also been accused of being unable to “function in the diverse and pluralistic environment” of the Naval Nuclear Power Training Command in Goose Creek, S.C.

The highly decorated, 19-year military veteran previously served in the Marine Corps and has had several high-profile assignments – including being named force chaplain of the Navy SEALs.

Just a few months ago, Modder’s commander called him “the best of the best” and a “consummate professional leader” worthy of an early promotion.

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But all that changed after Modder’s assistant, a married gay officer at the base who was upset about the minister’s views on same-sex relationships and homosexuality, filed a complaint against the chaplain.

The young officer had been working for the chaplain only for about a month when he began peppering him with questions about homosexuality.

“His five-page letter of complaint was unconscionable,” Modder told me. “It was insulting and it was devastating. I felt I discriminated against.”

Modder is also accused of:

* Telling a woman that she was “shaming herself in the eyes of God” for having premarital sex.

* Telling a student that homosexuality was wrong and that “the penis was meant for the vagina and not for the anus.”

* Berating an unmarried student for becoming pregnant.

Michael Berry, an attorney at Liberty Institute, a law firm that specializes in religious liberty cases, told me his client categorically denies making any such statements. He said the chaplain is the victim of a setup.

“I believe some of what the lieutenant has alleged could constitute a military crime – false statements, taking what the chaplain said and twisting or misconstruing it in an attempt to get the chaplain punished,” Berry said. “He abused the position he was placed in as a chaplain’s assistant.”

A spokeswoman for the Navy Chaplain Corps said Modder has been temporarily reassigned during the investigation into the allegations.

“The Navy values, and protects in policy, the rights of its service members, including chaplains, to practice according to the tenets of their faith and respects the rights of each individual to determine their own religious convictions,” Christianne Witten said.

Mike Huckabee, a potential candidate for the White House in 2016, wonders if it is “becoming illegal to be a Christian” in the military.

“Today’s military planners seem to think there should be nothing but atheists in foxholes, and that includes chaplains,” he told me.

Franklin Graham, president and CEO of the Billy Graham Evangelistic Association, defended Modder in a Facebook post.

“It’s a sad day in America when military chaplains have to choose between being true to their faith and keeping their jobs,” he wrote. “But this is what’s happening at every level under the Obama administration.” 

Rep. Doug Collins (R-Ga.), a Southern Baptist Air Force Reserve chaplain, told me he plans to raise the issue of Chaplain Modder with the Pentagon.

“The religious liberty issue in the military needs to stop,” Collins said. “The rulings are clear. As a chaplain we are provided to stay within the tenets of our faith. You cannot force me to counsel or to provide service outside the tenets of my faith.”

Like the Southern Baptist Convention, the Assemblies of God considers homosexual conduct to be a sin. So what happens when religious doctrine conflicts with military doctrine?

“I am an officer in the Air Force but I am endorsed by the Southern Baptist Convention,” Collins told me. “Without one, I cannot be the other.”

And that seems to be at the heart of the issue with Chaplain Modder.

“When you have the military imposing what seems to be an arbitrary line on when you can stand up for the tenets of your faith, it leaves chaplains in a very precarious position,” Collins said.

More than 40,000 people, meanwhile, have signed a Family Research Council petition urging the Pentagon to restore Modder to his position. 

“If you think chaplains have some of the safest jobs in the military, think again,” FRC President Tony Perkins said. “Men of the cloth are under some of the heaviest fire – and it’s coming from their own side.”

Sen. Ted Cruz (R-Texas) tweeted his support of Modder, lamenting that the chaplain is the “latest target in a series of assaults on religious liberty” in the military and across the nation.

Rick Santorum, who is also considering a White House bid, said Modder’s plight is evidence that “religious liberty in our country is under assault.”

And what’s even more disturbing is the possibility that a gay officer may have intentionally targeted a Christian chaplain who follows the teachings of the Bible regarding issues of sexuality.

If you don’t want the counsel of a Christian chaplain – don’t go to a Christian chaplain.

Todd Starnes is host of Fox News & Commentary, heard on hundreds of radio stations. His latest book is "God Less America: Real Stories From the Front Lines of the Attack on Traditional Values." Follow Todd on Twitter@ToddStarnes and find him on Facebook.