The headmaster of a Christian school in Washington has been arrested for allegedly raping and molesting two female pupils, aged 10 and 11, today.

Detectives arrested Douglas Allison, 55, at his home on Tuesday night.

Allison was investigated by police after a 10-year-old girl who attends his school, Mountain View Christian School, told her parents he had sexually assaulted her multiple times at the school.

During the investigation, another victim who attended the school was uncovered. Police do not think there are any other victims at the school, which is run by the Seventh-Day Adventist Church and has around 13 pupils and one teacher – Allison's wife. His wife is not under investigation. 

"The second victim disclosed to detectives she had been sexually assaulted in a similar fashion by Allison," the police said in a press release.

He has been accused of four counts of first-degree child rape and 12 counts of first-degree child molestation and is being held at Clallam County Corrections Facility.

A church spokeswoman, Becky Meharry, has said Allison, who taught grades 5 -8, has been placed on administrative leave pending the investigation.

"We just want you to know that the health and safety of our students is of course our priority" Meharry told Q13 Fox news.

"As soon as we were notified by the police that there was an investigation underway the principal was put on administrative leave. We are taking care of our students by putting in respected and trusted teachers to take over the teaching responsibilities, and providing counseling and car for families that have been affected."

A formal charging decision is expected to be made by Clallam County Prosecuteor's Office by Friday.