Fr Michael Creagh, 56, former deputy house master at the Douai Abbey School, in Berkshire, was jailed for nine months after pleading guilty at Reading Crown Court to three counts of indecent assault.
After the case detectives from the Reading family protection unit alleged the school had hindered their investigation by withholding information about the priest and other pupils he was suspected of abusing.
Det Sgt John Kellagher, said: 'The school knew all along but took weeks to give us details of the boys we wanted to interview.'
The court heard Creagh began a sexual relationship with the boy in 1988, soon after the child arrived at the pounds 2,500-a-term boarding school run by Benedictine monks.
Anthony King, for the prosecution, said the boy was assaulted over a period of nine months and had tried to stop the priest's advances. The first assault was said to have taken place when the child sought counselling about the onset of puberty. Mr King said on another occasion the priest put his hand down the boy's trousers and masturbated him after he asked for his weekly pocket money; on another night, Creagh masturbated his victim after ordering his classmates to leave the school television room.
Mr King said Creagh persuaded the child's parents to allow him to visit their home abroad. While the parents were away, the priest attempted a further attack, which the child resisted.
'The boy was embarrassed and confused by the actions of a man who was not only a monk but his house master,' Mr King said.
Martin Hall-Smith, for the defence, said Creagh was bitterly ashamed. There had been no element of coercion in the priest's advances, which Mr Hall-Smith blamed on pressure of work.
Judge Stanley Spence, sentencing Creagh, told him: 'You were a member of a religious community and in a position of trust - in loco parentis for that child.
'What is particularly reprehensible is that the child sought counselling when he came to you about signs of puberty. It was a double betrayal of trust.'Reuse content