The Archbishop of York has said he is deeply ashamed that the Church of England failed to ensure children were not abused by a former cathedral dean.

John Sentamu was responding to a report published on Wednesday into the handling of allegations of sex abuse against the late Robert Waddington, formerly dean of Manchester, which found there were systemic failures by the church.

Sentamu’s predecessor as archbishop, Lord Hope of Thornes, has been accused of failing to act on information he received.

The report, by Judge Sally Cahill QC, found that: “Our conclusion, having heard his [Lord Hope’s] evidence, is that his concern for the welfare of Robert Waddington seems to have been paramount in his response to these allegations.”

Hope has said he is disappointed that the report raised concerns about how the cases were handled and denied that there was a cover-up.

Responding to the report, Sentamu said: “I have already been in contact with those who gave evidence to the inquiry regarding their alleged abuse by Robert Waddington.

“As I have said to them, I am deeply ashamed that the church was not vigilant enough to ensure that these things did not happen, failing both to watch and to act, where children were at serious risk.”

The archbishop said he accepted the report’s conclusion that “irrespective of policies in force, there was a systemic failure”.

He said: “Although the report notes no one has come forward to say they were abused by Robert Waddington after the first complaint was made in 1999, what stands out is that between 1999 and 2004 those in senior positions responsible for taking decisions in these matters were ’not qualified or sufficiently experienced in child protection’.”

Hope has denied suggestions that he covered up allegations against Waddington, who died from cancer in 2007.

On Wednesday he said: “I have maintained throughout my career that any allegation of abuse made against anyone connected to the church must be dealt with professionally and swiftly.

“Accordingly, I am obviously disappointed that this inquiry has raised concerns about how the two cases in questions were dealt with during my time at Bishopthorpe [seat of the archbishop of York].”

Hope said that when allegations were reported to him 15 and 12 years ago, they were unspecific and he has never been told the full details.

He said there was no recommendation at that time that allegations should be reported to the police and he was told the complainant would not talk to officers.

The former archbishop withdrew Waddington’s permission to act as a priest in 2004.

He said: “Last May, in some of the reporting, it was suggested that there had been some cover-up by me.

“This report makes clear that not applying the policy is not the same as a cover-up.

“Hindsight is, of course, a wonderful thing. If all that has been learned by organisations and the public about child abuse in the last 15 years had been known in 1999 and 2004, I would certainly have acted differently.” Hope added: “If either of the two persons concerned feel in the light of this report they have been denied the justice they deserve, then, on behalf of the church, I offer my personal and profound apology.

“I genuinely believed that any complaints were being adequately dealt with by the respective dioceses in which they were alleged to have happened.”

One of Waddington’s victims, Eli Ward, who has waived his right to anonymity, said his abuser was a “very clever guy”.

Describing how he was groomed, he told BBC News: “It would progress to picking me up, go to his house, stay over and then stay in his room and so on.

“Over a period of time, little by little, very strategic planning, very clever guy, peeling away his victim … not just an opportunity – take it, it’s very much insidious, planning and grooming, very clever.”

Responding to the report, he said: “I want no other child, person, to go through what I have gone through.

“I have been through the full range of emotions – that’s terrible, disgraceful. I should have been enjoying life, getting on with it – my abuse has stopped me doing that.”

Cahill made it clear in her report it was not within her remit to decide on the truth of any of the allegations against Waddington.

Those who made allegations described abuse in Manchester, York, London, Carlisle and in Queensland, Australia dating back as far as the 1950s.