Writing in Soldier Magazine, Major Ross McCleod of the Royal Signals claimed that having a senior officer's whole team at prayers or carol services made them look better when going for promotion.
But requiring troops to attend church services breaks the rules.
Major McCleod wrote: "I fear I may have acted unlawfully and that some colleagues continue to do so mainly for career preservation purposes."
Writing in response to Major McCleod, Rev Jim Francis, staff chaplain pointed to the Queen's Regulations which state that "no one is to be compelled to attend divine service against his or her wishes".
Speaking on Premier's News Hour, retired Major Rhett Parkinson from the Armed Forces Christian Union said that, in his experience, a lot of soldiers wanted to attend church services.
He said: "It was very much an option - soldiers particularly on operations are more open and more keen to get involved with what the chaplains do."
Major Parkinson added: "There is definitely times when people may feel under peer pressure to go but long gone are the days where a commanding officer would go to church on a Sunday... not many would go out of choice.
"There is an awkward situation where I've had friends who've practiced their Christian faith and they face a real dilemma as to how to share their faith in a way that doesn't create that peer pressure that makes soldiers feel they have to go to church on Sunday."
Premier has reached out to Major McCleod and the Ministry of Defence for comment.
Listen to Aaron James speaking to Major Parkinson here: