He was also placed on the sex offenders register and ordered to pay £2,000 to each of the three former choristers who he abused between 1985 and 1990.
His case has provoked controversy after media reports suggested that the Church of England covered up Halliday's activities by allowing him to leave without contacting the police.
A report on the Today programme this morning alleged that the church had allowed the choirmaster to leave on the proviso that he had no further contact with children after one of the victims came forward in 1990.
The church has defended its child protection policies and suggested that the policy on safeguarding children has changed significantly since 1990.
A spokesman for the Guildford Diocese, Mark Rudall, said in a statement: "We are completely satisfied that what was done at the time was the way things happened in those days when child protection awareness was on the cusp of serious change."
He added that he "trusted that there has been some closure" to the victims and their families from today's sentencing and said that had the situation occurred now then the church would have dealt with things "very differently".
"There were no solid guidelines in those days," he said.
The Church of England added in a general statement published on its website this morning that it was "committed to the safeguarding, care and nurture of the children within our church community".
"We respond without delay to every complaint made, that a child or young person for whom we are responsible may have been harmed, and fully cooperate with statutory agencies during any investigation they make into allegations concerning a member of the church community," it added.
Earlier, speaking to the Today programme, the Reverend Pearl Luxon said church policies had been strengthened since the abuse by Halliday took place.
"These matters are always reviewed after they occur and we learn from our mistakes and our good practice is improved at all stages," she said.
"Our robust policies are improved through learning from the past and through following the guidance and good practice that happens now."
The court heard that the abuse occurred in Hampshire while the victims were on camp, after swimming and at Halliday's home.
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