Peter Halliday, 61, from Farnborough, Hampshire, abused the three boys who were in his church choir between 1985 and 1990
He pleaded guilty to 10 counts of indecent assault at an earlier hearing and was jailed at Winchester Crown Court.
Judge Ian Pearson said that Halliday had systematically sexually abused the boys and said the offences were so serious only a custodial sentence was appropriate.
He also banned married Halliday from working with children for life and told him that he would be put on the Sex Offenders Register for life and ordered him to pay £2,000 each compensation to his victims.
The court was told that one of the boys told a Christian leader at a camp that Halliday had been abusing him, and a local vicar, Alan Boddington, was informed.
The boy’s father and the Rev Boddington then confronted Halliday, who admitted he had abused the boy. But Susan Evans, defending Halliday, said that the vicar was only aware of one allegation at the time, and the parents of the boy did not want to go to the police.
“In my submission there was good reason in this case for the Rev Boddington to act as he did,” said Miss Evans. She said that Mr Boddington and Halliday’s wife then effectively placed Halliday “on probation” and he was told to leave as choirmaster of St Peter’s Church in Farnborough with immediate effect.
He was also told to resign from the church and receive counselling, which he did with his wife.
Miss Evans told the court that Halliday was also told that he could never work with children again, and she said he had never done so, and has only worked with an adult choir from 1997. She said that he had been on the board of governors of a secondary school from 1988 to 2000 but had no unsupervised contact with children during that time.