U.S. military commanders in Afghanistan on Thursday ordered the removal of a steeple and crucifix erected over a remote American base in the Muslim country after a soldier deployed there noted that the symbols violated Army regulations, and could reinforce suspicions that the United States is fighting a holy war.

It is unclear how long ago the Christian symbols at the chapel at Forward Operating Base Orgun-E had been in place. In terms of religious displays, they are hardly ostentatious — a cross on a small rooftop steeple and cross-shaped windows in the doors. But Sgt. Joel Muhlnickel was alarmed by the symbolism at Orgun-E, especially the cross that rises up over the rooftops at the base.

"When I think of an army sporting a Christian cross, I think Crusades," Muhlnickel wrote on Facebook from Orgun — a message that was forwarded to NBC News by a third party. "Neither my country nor my army force me to swear allegiance to Odin, Jesus, Buddha or Horus. Freedom from religious oppression is pretty much the reason why the United States was founded."

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"It is the sort of thing that provides a boundless bonanza of terrorist propaganda for the mujahedeen, the insurrectionists, the Taliban and al-Qaida that we are supposedly fighting to protect our national security," said Mikey Weinstein, founder and president of the non-profit Military Religious Freedom Foundation. "The message of the cross on the chapel is basically putting out the message in Pashto, Dari and Arabic to please blow me up because I'm a latter day Christian crusader."

The U.S. military provides chapels for troops around the world and has thousands of chaplains deployed — the majority of them Christian, while there are also Jewish, Muslim and other faith leaders.

Chapels are set up even in outposts as far-flung as Orgun-E.

But Army regulations state that these facilities — usually nondescript temporary structures — are to be neutral gathering spaces, not dedicated to any one faith, except when being used for a specific worship service. Portable symbols, icons or statues can be used during religious services, but then must be removed or covered up for others who use the space.

"In general the chapels have to be ecumenical so they can be converted from one religion to another," said Elizabeth Hillman, professor of law at University of California Hastings College of Law and President of the National Institute of Military Justice. "To create permanent structures that evoke one particular religion — that is problematic.

"I would think that anything that would increase the vulnerability of a forward operating base is a problematic," Hillman added.

Muhlnickel raised his concerns through his chain of command, and then — unconvinced that it would result in action — turned to outside organizations, including the nonprofit American Atheists.

"Chaplains know the regulations very well," said Justin Griffith, an Army sergeant at Fort Bragg, N.C., and military director for American Atheists in his personal time. "Whoever authorized (the steeple and crosses) knew exactly what they were doing. It's intentionally disrespectful to the non-Christians in the U.S. military ... Put it in Afghanistan, the danger is very real, to personnel, even to Christians."

The Army, contacted by NBC on Tuesday morning, responded to queries Wednesday afternoon, saying the cross had been removed and boards had been placed over the cross-shaped windows while the base ordered new doors.

"The local command in Afghanistan is aware of this chapel and has taken appropriate action to ensure that it is changed into a neutral facility," said a statement from an Army Spokesman at the Pentagon.

Hours later, Orgun command sent out a memo throughout the base explaining that the chapel was to be brought into compliance by eliminating the crosses, and assuring soldiers that it would be handled in a respectful manner.

Griffith, an atheist who often calls out practices that he believes cross the line from the free exercise of religion to unconstitutional proselytizing or discrimination, has learned that his views are unpopular with many in the military. He's concerned about Muhlnickel suffering reprisal. 

"Sgt. Muhlnickel’s efforts just put the pin back in the grenade," said Griffith. "The military now needs to protect him from any backlash ... and not punish him for speaking out against the dangerous 'crusader' symbolism."

In similar situations that have come to light, military commanders have ordered the removal of the religious symbols. In April 2012, when a Marine Corps squadron revived the "Crusaders" name with the shield and cross logo for fighter jets, the Military Religious Freedom Foundation challenged the move, citing constitutional and security concerns. The next month, the Marine Corps said that the squadron had converted back to the moniker "Werewolves," replacing the logos from the jets, uniforms, buildings and elsewhere.

A chapel at Camp Marmal, another U.S. base in northern Afghanistan, was ordered to remove a large cross from its chapel after complaints, Politico reported. A spokesman from the Pentagon agreed that the Camp Marmal cross had violated Army regulations.

In Afghanistan, where the population is more than 99 percent Muslim, the tiny Christian population worships in secret, out of fear of attack by extremist Muslims. Christian evangelism is illegal in the country, and foreigners suspected of spreading Christian teachings have been deported by the government, and attacked and kidnapped by extremists.

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