Thousands of people are rallying behind the Navy chaplain who lost his position after asserting biblical beliefs in private counselling sessions.

Lt. Cmdr. Wes Modder is at risk of being discharged because of alleged insensitivity towards premarital sex and same-sex relations.

The lieutenant commander's superior officer issued a memorandum accusing Modder of failing to "show tolerance and respect" at the Naval Nuclear Power Training Command in Goose Creek, South Carolina.

"On multiple occasions he discriminated against students who were of different faiths and backgrounds," Captain Jon R. Fahs wrote, adding that Modder was unable to "function in the diverse and pluralistic environment" of the training command.

Modder was accused of telling a woman having premarital sex that she was "shaming herself in the eyes of God," telling a gay person that "the penis was meant for the vagina and not for the anus," and criticising an unmarried pregnant woman.

Michael Berry of the Liberty Institute, who represents Modder, said that his client denies the allegations. A gay assistant of Modder levied the claims in a five-page letter.

"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 of the junior officer's allegations.

"He abused the position he was placed in as a chaplain's assistant."

Rallying behind Modder is Billy Graham Evangelistic Association president and CEO Franklin Graham.

"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 on Facebook. "But this is what's happening at every level under the Obama administration."

Former Arkansas governor Mike Huckabee also voiced support for the chaplain.

"Today's military planners seem to think there should be nothing but atheists in foxholes, and that includes chaplains," he told Fox News.

Sen. Ted Cruz, Rep. Doug Collins, former senator Rick Santorum, and other politicians also spoke in favour of reinstating Modder, and over 50,000 people have signed a petition urging the Pentagon to intervene in the case.