The Archbishop of Canterbury, Dr Rowan Williams, has expressed his deep sorrow over the suffering experienced in child abuse cases involving the Church of England after a former choirmaster was sentenced to two-and-a-half years in prison this week for abusing boys in his care.

Peter Halliday, 62, formerly a choirmaster in Farnborough, Hampshire, admitted indecently assaulting boys under his care between 1985 and 1990. He was sentenced by Winchester Crown Court to two-and-a-half years in jail on Thursday and ordered to pay £2,000 to each of his three victims.

Dr Williams said that the Church had developed greater awareness and expertise, and had stringent procedures in place, but that vigilance was crucial.

"Any case in which the Church has failed to prove itself a safe place for children is deplorable. This is one such case, and we can only express our keen awareness of the damage and deep sorrow for the suffering caused."

The Church of England was strongly criticised for failing to report the abuse to police when church authorities were first made aware by the parents of one victim in 1990.

Halliday was instead told he should leave quietly and agree that he would have no more contact with young children. He went on, however, to work with young boys when he became a singer in the Royal School of Church Music.

Independent Christian charity, the Churches Child Protection Advisory Service, said the Church of England had "seriously mishandled" the situation, criticising in particular the Church's failure to notify police of the abuse and to remedy previous inaction when it later implemented its child protection programme.

"It is also misleading to suggest that there was only one opportunity to act in this case," said the CCPAS. "The introduction a few years later of the Church of England's child protection policy and their training programme should have highlighted to those concerned the inappropriateness of actions previously taken and this should have resulted in a different response."

The Archbishop of Canterbury said: "The principle that the welfare of the child must always take priority has sometimes been misunderstood to mean that a child should not be put through the distress of public legal procedures. It appears to me that this misunderstanding may have been involved in this instance."

He said that in the period since the abuse took place, the Church of England had developed greater expertise and implemented "far more stringent procedures".

"This does not help victims of an earlier era, but the awareness of the cost they have borne is something that underlines the imperative need to keep all our procedures in the strictest working order," he said.

The Diocese of Guildford expressed regret and sadness over the child abuse by Halliday but said it was "completely satisfied" with the way it had handled the abuse charges at the time.

"Church officers at every level acted in good faith in accordance in what they perceived to be in the best interests of child and family - at that time, in that setting - before the law and government guidelines were as they are today," said diocesan spokesman, the Rev Mark Rudall.

He added that child protection policy within the Church of England was under constant review and expressed his hope that Halliday's sentencing today had provided "some kind of closure for what must have been many years of background distress to their lives".

In a statement released Thursday, the Church of England reaffirmed its commitment "to the safeguarding, care and nurture of the children within our community" and offered reassurances that those working with children are properly vetted by police.

"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 co-operate with statutory agencies during any investigation they make into allegations concerning a member of the church community," it said.