The Archbishop of York, Dr John Sentamu, announced on Saturday afternoon that an independent inquiry is to be set up into allegations that a former Archbishop of York, Lord Hope of Thornes, failed to report allegations of child abuse, either to the police, or to independent child protection agencies.

A joint investigation by The Times in London and The Australian newspaper in Sydney, published on Friday, reports that Lord Hope was told of accusations against the Very Revd Robert Waddington (above), a former Dean of Manchester Cathedral, in 1999 and in 2003. He removed the Dean's permission to officiate in 2005 but did not report the allegations to the police or child protection authorities. Robert Waddington, who was Dean of Manchester from 1984 to his retirement in 1993, died in 2007.

The statement from Dr Sentamu's office says that the Archbishop is "in the process of setting up an Independent Inquiry specifically into the issues surrounding the reports relating to alleged child abuse by the late Robert Waddington".

It continues: "When any church related abuse comes to light, the Church's first concern must be for the victim offering support and apologising for the abuse, acknowledging that the effects can be lifelong. When the Inquiry makes its report the Archbishop will make its findings public. The Church of England continues to review its Child Protection and Safeguarding policies regularly to ensure that the Church is a safe place for all. Child abuse is a heinous and personally damaging crime, it is therefore incumbent on the Church to treat such matters with the utmost seriousness."

The inquiry's terms of reference and membership would be announced in due course, the statement said.

Allegations of abuse were first made in England in 2003 by the family of a former chorister at Manchester Cathedral, Eli Ward. The Rt Revd Nigel McCulloch, who was Bishop of Manchester from 2002 until his retirement this year, was made aware of the allegations by the diocesan child protection adviser, but a diocesan child protection report claimed that "little could be done" unless the victim himself came forward.

On Friday, Bishop McCulloch said he had been "shocked and saddened" to learn of the allegations. He had asked his chaplain to contact the child protection officer for the diocese "in order that the correct procedures following such allegations could be properly followed".

Bishop McCulloch also reported the matter to Lord Hope, who asked the child protection officer to contact him. Bishop McCulloch said on Friday: "The child protection officer, having been told by the members of the family who had made the allegations that the alleged victim did not wish the matter to be reported to the police, urged them very strongly to do so. In responding to and reporting this tragic alleged abuse, I believe that I and the child protection officer followed correctly the then current 1999 guidelines laid down by the Church of England." 

At this time, Lord Hope was aware of previous allegations against Dean Waddington from Australia, where Dean Waddington was Headmaster of St Barnabas School, Ravenshoe, from 1961 to 1970.

The Australian reports that, in 1999, Bim Atkinson told the Rt Revd Clyde Wood, then Bishop of North Queensland, Australia, about years of abuse at the hands of Dean Waddington, while he was a pupil at St Barnabas. Bishop Wood reported the allegations to the Rt Revd Christopher Mayfield, Bishop of Manchester from 1993 to 2002, who said that Waddington had retired in 1993. Lord Hope was then told and he confronted Dean Waddington.

In 1999, Lord Hope wrote to Bishop Wood saying that Dean Waddington was "shocked and distressed" by the allegations and that Church records showed no "hint of such behaviour throughout the time of his ministry here in England".

Lord Hope wrote of Dean Waddington: "He was clearly shocked, and indicated to me that, whilst he may have acted at times in a way which could have been misinterpreted, he could not recall any particular incident or incidents which were of the 'seriousness' which you describe in your letter.

"He said he was deeply sorry for anything he may have done so to offend, and wished to extend an unreserved apology to the young man concerned and to make it very clear that there is no question of any such behaviour occurring again."

Mr Atkinson said that Bishop Wood had told him that Dean Waddington had denied everything and was close to death. Mr Atkinson asked for a copy of the letter from Lord Hope before "relinquishing the Anglican Church" from any responsibility for the alleged abuse. Bishop Wood then wrote to Lord Hope: "I can only hope and pray that this matter now having been raised, and Father Waddington being traumatised by the receipt of the allegations, that now notice of closure from this end, will not leave Father Waddington permanently distressed by this matter."

In 2002, learning that Dean Waddington was still alive, Mr Atkinson made a complaint to the police. He was joined by a fellow pupil, who made similar allegations. Police said that there was not enough evidence to extradite Dean Waddington to Australia.

Mr Atkinson continued to press for an investigation. In 2005, the Anglican Professional Standards Committee wrote to him saying that it did not believe that "spending a huge amount of money on another investigation will benefit anyone". Mr Aktinson received a £50,000 compensation payout from the Church but no admission of liability.

The report compiled by the diocese of Manchester after the allegations made by Mr Ward's family in 2003 refers to a "previous referral about sexual impropriety some time ago from Australia, where RW had been the headmaster at a school. An ex-pupil had made a complaint to the Bishop of (north) Queensland who had relayed it to the Archbishop (of York)."  Mr Ward's family was not told about this, and the report says that Bishop McCulloch considered telling the family that Dean Waddington was ill, a course of action rejected by diocesan staff.

On Thursday night, Lord Hope, who was Archbishop of York from 1995 to 2005, said: "I strenuously deny (and am obviously disappointed at) the suggestion that myself or my team at the time would have acted negligently in this or any other safeguarding matter."

Throughout his time as bishop and archbishop, he had "always adhered to the statutory practices of the Church of England concerning safeguarding", which, at the time, stated that there was "no automatic legal obligation on the Church to refer allegations by adults to the police or social services."

Lord Hope said: "In considering whether children would be at risk from Robert Waddington I decided under these guidelines that this would not be the case, given his serious ill health following cancer surgery. The following year I revoked Robert Waddington's permission to officiate. He died two years later."

He was "deeply aware of the pain caused to any victim of child abuse, especially at the hands of a trustworthy person within the Church".

Greater Manchester Police was not made aware of the allegations until last year, when Mr Ward made a report to officers. He has begun legal action against the diocese of Manchester.

On Friday, a spokesperson for the office of the Archbishop of York confirmed that the Dean and Chapter of Manchester Cathedral had received a "letter of claim" which had been referred to its insurers and solicitors. This letter had not been seen by the Archbishop of York, Dr Sentamu, who would therefore not comment. A statement from the diocese of Manchester said that it was "working cooperatively with the parties concerned".

A statement from Manchester Cathedral said: "We are shocked and saddened by the nature of these allegations relating to events in the early 1980s. We want to reassure parents and congregation members that for a number of years Manchester Cathedral has had in place a robust child protection policy with CRB checks made on all clergy and those who work with specifically with children."

Bishop McCulloch said: "This is a particularly sad story of abuse that has brought deep and lasting distress to a young boy who had put his trust in the Church. Since 2004 new guidelines for responding to allegations of abuse have replaced those of 1999. All such allegations are now reported automatically to the police by the Church. I express my sympathy with all who are victims of such unacceptable and damaging behaviour and urge those who are made to suffer in this way to report the matter to the police." 

On Friday, the Bishop of Southwell & Nottingham, the Rt Revd Paul Butler, who chairs the Churches National Safeguarding Committee, said: "When any church-related abuse or allegation of abuse comes to light our first concern is always for the victim. . . As a Church we will always apologise for past systems that let down the vulnerable and offer support to anyone whose life has been affected.

"Today we have robust safeguarding policies in place and although we can never be complacent, we remain committed to ensuring that the Church is a safe place for all. We would encourage anyone who has any safeguarding concerns within a church context to come forward, with the assurance they will be listened to."

The current safeguarding guidelines for The Church of England (Protecting All God's Children, 2010) state that: "People who have committed sexual abuse against someone years ago could well be abusing children today. The individual survivor should be encouraged and supported to report the matter to the police if this has not already been done." 

Dean Waddington, born in 1927, joined the The Oratory of the Good Shepherd (OGS), an Anglican religious order of celibate clergy, in 1960, becoming the Superior in 1987. He was a Canon Residentiary at Carlisle and the Bishop's Adviser for Education from 1972 to 1977, when he was appointed the general secretary of the General Synod's Board of Education.

An obituary for the Church Times described him as "full of contradictions. He was contemplative, private, and sometimes depressed . . . He preferred simplicity and avoided ostentation; and yet could suddenly splash out on a 'flashy car'." He was, the obituary claimed, "always the teacher", his sermons to children "instructive fun".

Mr Ward told The Times of how the abuse by Dean Waddington had caused an "identity crisis" in his life: "It feels to me now that the things I love today, they're all linked to him. . . I come from Salford but I speak like this because of him. I come from a very poor background but yet people think I'm a wealthy individual or I've gone to public school. This is the identity crisis that I've had and still have because I don't know who I am."

The Bishop of Queensland, the Rt Revd William Ray, has said that he will refer the handling of the case to the General Synod and Australia's Royal Commission into institutional child abuse, established this year.