The Church's interim safeguarding director has began a complaint process against Dr Peter Forster under the Clergy Discipline Measure (CDM).
Such procedures can usually only be filed within twelve-months of alleged misconduct but it is understood Sir Roger Singleton is seeking an exception. The complaint has not yet been lodged.
The complaint would focus on Dr Peter's (pictured) response to a letter sent to him in 2009 by Warrington vicar Charles Gordon Dickenson who, in the note, confessed to child abuse.
Despite the admission, Mr Dickenson was permitted to stay on as a retired clergy member and hold services for another five years.
The 89-year-old was jailed last month after admitting eight counts of sexual assault against a boy during the 1970s.
The Diocese of Chester subsequently issued an "unreserved apology" to Mr Dickenson's victim. Bosses accepted failing to act on information it had received concerning him.
It is unknown whether Dr Peter was personally aware of the letter.
The complaint will be overseen by the Archbishop of York. Dr John Sentamu is due to set out in 28 days whether it will be acted upon or dismissed.
He could insist the complaint be kept on file for up to five years or issue a penalty - which might include a rebuke to prohibition for life.
Premier reported last month on news the Diocese of Chester would be the subject of an independent review by the Church of England's National Safeguarding Team. The review and the CDM complaint are separate.
In light of the review, Dr Peter said he was handing over responsibilities for safeguarding in his diocese to the Bishop of Birkenhead.
He said: "I have taken this decision in response to recent comment into my handling of the Gordon Dickenson case in 2009.
"An independent review will seek to identify where any failures in procedures arose, and what lessons can be learned and I look forward to contributing to the review and to giving a full account of my actions in relation to this matter.
"The Diocese of Chester takes seriously its safeguarding responsibilities at every level. Whilst an independent review into my actions takes place, I recognise that I should not continue to lead the safeguarding arrangements in the Diocese.
"I will continue in all other duties relating to my role of Bishop of Chester.
"I will not be making any further public comments in relation to this matter until the outcome of the independent review."
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