Lord Hope of Thornes was told of the accusations against the Very Rev Robert Waddington, a former Dean of Manchester Cathedral who was made responsible for Church schools, in 1999 and then again in 2003.
Internal reports within the Church show that Right Rev Nigel McCulloch, who was the Bishop of Manchester at the time, was aware of the allegations made by the family of a former cathedral chorister in 2003.
He then reported to the matter to his immediate superior, the Archbishop of York, as well as to his diocesan child protection officer.
Lord Hope, who was Archbishop of York from 1995 to 2005, did not take the allegations any further. However, he denied a cover-up, saying he had followed the procedure in place at the time.
He said: “I would strongly resist any suggestion that I was in the business of covering up anything. I would absolutely deny that. There’s no way I was interested in any cover up.”
Greater Manchester Police have expressed concerns that the case was not reported to them while Waddington was still alive. The former dean died of throat cancer in 2007.
The force was only made aware of the allegations when a former Manchester choirboy, Eli Ward, reported his abuse to officers.
Mr Ward said this past week: “After so many years of suffering alone, I find myself in a position where the more research I do, the more shocking the cover-up of the Church.”
Mr Ward, 40, said he was groomed and abused by Waddington in the 1980s when he was a chorister in Manchester. He is taking legal action against The Diocese of Manchester.
The Diocese of Manchester said that it was aware of “allegations of abuse from the past against a former dean of Manchester Cathedral and we are working co-operatively with the parties concerned”.