The former Archbishop of York, Lord Hope of Thornes, has resigned from ministry in the Church of England after an inquiry found that there had been "systemic failures" in the Church's handling of the case of a paedophile priest.

The report by Judge Sally Cahill QC into the case of Robert Waddington, the former Dean of Manchester, who abused choirboys and school pupils in York, Manchester, London, Carlisle and Australia over 50 years, was commissioned by the current Archbishop of York, Rt Rev John Sentamu.

Lord Hope was criticised in the report for not referring accusations to police or to child protection agencies, though he revoked Waddington's right to conduct services.

It identified 18 breaches of church policy, including failing to make records of his conversations with Waddington, not seeking help from his child protection adviser and failing to establish if there was a continuing risk to children. Judge Cahill said the failings meant that "opportunities were missed" to start an enquiry.

Lord Hope said: "After much prayerful and considered thought I wrote at the beginning of the week to the Bishop of Leeds and in the light of the Cahill Inquiry Report I have submitted my resignation as Honorary Assistant Bishop of Bradford, now West Yorkshire and the Dales, with immediate effect.

"This ends my nearly 50 years of formal ministry in the Church of England, which I have always sought to serve with dedication.

"I will certainly continue to pray for the important ongoing work with survivors."

When the report came out he strongly denied covering up abuse but offered a "personal and profound apology" to the victims. He said there was no recommendation at the time that allegations should be reported to the police, adding: "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."

The current Archbishop of York, Rt Rev John Sentamu, has expressed shock and dismay over the Waddington case. He paid tribute to Lord Hope, saying: "I am deeply saddened by his decision. He has served the Church of England with joyfulness, commitment, honesty and holiness.

"I personally thank him for his leadership as a priest, principal of a theological college, bishop and archbishop of the Province of York; and above all as a dear brother in Christ."