Victor Franz Jagerstatter, 39, was arrested by Mountain Home Police Friday.
The victim, an airman stationed at the Mountain Home Air Force Base, told investigators that he was raped July 9 after he returned home from a night of drinking and passed out.
Police said that the victim and the suspect knew one another, but did not have a sexual relationship, and the victim had not given Jagerstatter permission to have sexual contact with him.
Court documents reveal that the airman reported the assault to Air Force family advocate officials. Mountain Home Police spokeswoman Melanie Broughton said it was turned over to detectives with the Office of Special Investigation July 11.
"They investigated it and found that there was probable cause, which means that it's more probable than not that this occurred, so we go forward," Broughton said. "We take theses things seriously, and we investigate them thoroughly."
Roman Catholic Diocese of Boise spokesman David Llamas released a statement saying the church was aware of the charge.
"The Roman Catholic Diocese of Boise has learned of the arrest of Rev. Victor Jagerslatter, Parish Administrator of Our Lady of Good Counsel in Mountain Home," he said in a statement. "The Diocese will cooperate fully with law enforcement officials in their investigation. Due to the seriousness of the allegations, Fr. Jagerstatter has been placed on administrative leave. We hold up in prayer all those involved in this matter."