The Catholic Bishop of Clogher has admitted he made a mistake over 20 years ago when he agreed to keep a case of clerical sex abuse secret at the request of the victim's family.

Most Rev. Dr. Joseph Duffy was told about the abuse carried out by the then Fr. John McCabe in 1989 but did not report it to the police because the victim's parents were devoutly religious and did not want the matter taken any further for fear of damaging the reputation of the church.

McCabe was forced to resign from the priesthood around Easter of the following year. He taught English at St. Michael's College in Enniskillen from 1977 until 1988, when he left due to ill-health following a heart attack. A number of years later the police were informed about the case and just before Christmas 1995 McCabe appeared at Enniskillen Crown Court and pleaded guilty to 13 charges of indecently assaulting a boy between 1979 and 1985, from when his victim was nine until he was 15. He was jailed for 20 months.

In the midst of the on-going controversy over the Catholic Church's handling of clerical sex abuse and the media feeding frenzy it has generated the McCabe case resurfaced in two Sunday newspapers.

Responding to the stories Bishop Duffy pointed out that "the facts concerning the handling of this case have been in the public domain for at least 15 years". He described some of the reporting as erroneous and mistaken and emphatically denied the "untrue" allegations. In a statement the Church explained that the parents of the abused child in this instance had strongly requested confidentiality.

"Bishop Duffy felt it proper at the time to respect this request and admitted that this was mistaken on his part. If it happened now, the new protocol demands immediate reporting to the statutory bodies and this is what he would do. Bishop Duffy co-operated fully with the police when the parents of the abused placed the allegation in their hands," it added.

The dangers of keeping the case confidential were recognised by the judge at McCabe's trial in late 1995.

The court heard that McCabe befriended the victim's parents at a religious retreat at Benburb Priory in 1979 and then spent nights with them at their home in Belfast. It was there, while sharing a bedroom with their nine-year-old son, that the abuse began. It continued when McCabe brought the boy on holiday to Fermanagh and they stayed at the residential accommodation at St. Michael's College. By 1985 the boy was 15 and realised what was happening was wrong and the abuse stopped. However, he began to experience considerable emotional problems and his concerned family took him for counselling.

The family eventually learned what had been happening and in October 1989 the boy's mother, who was very fond of McCabe, confronted the priest. He refused to deny the allegations. The parents then went to Bishop Duffy and told him what had been happening and within six months McCabe had been forced to resign from the priesthood.

At his trial Judge David Smith asked why, when the family had confronted McCabe with the allegation in 1989, it had taken until 1995 for the case to come to court. He said people might think there had been a cover-up.

The prosecuting counsel explained that the boy's parents were devout Roman Catholics and just did not want the matter to come to light.

The judge stated: "No doubt that placed the Bishop, to whom they complained, in a very difficult position." The prosecutor said neither the boy nor his parents had made a complaint to the police and McCabe might well have escaped prosecution and punishment if he had not been curious as to how the boy was rehabilitating. Social services became suspicious and the police were called in.

In response to the renewed criticism of his handling of the McCabe's case Bishop Duffy acknowledged that it has taken Church leaders "a long time to come to an understanding of the real horror and pain of the experience of sexual abuse for the abused themselves and for their families".

He said it was a "great relief" to him to have the authorities share responsibility for dealing with allegations of clerical sex abuse.

"In the past Church leaders mistakenly took the view that they had full responsibility for handling abuse cases with all their complexities. Now the rightful role of the statutory bodies (police and social workers) is recognised in seeking to bring justice and healing to those affected by this heinous crime," Bishop Duffy stated.

Bishop Duffy is the latest senior cleric to admit to his role in covering up the activities of paedophile priests.

On St. Patrick's Day the Catholic Primate of Ireland, Cardinal Sean Brady, apologised for what he described as "a painful episode" from his past when, as a priest in 1975, he was at meetings where children signed vows of silence over complaints against serial abuser Fr. Brendan Smyth and the matter was not reported to police.

"Looking back, I am ashamed that I have not always upheld the values that I profess and believe in," the Cardinal admitted.

Meanwhile the Bishop of Derry, Dr. Seamus Hegarty, has been accused of having covered up a complaint with an out-of-court settlement containing a confidentiality clause and delaying reporting another case to the police.

And yesterday (Wednesday) the Pope accepted the resignation of an Irish bishop found to have mishandled allegations of clerical sex abuse in his County Cork diocese. Bishop John Magee stepped aside in March 2009 after an independent report found his Cloyne Diocese had put children at risk of harm.

It has also emerged that in 1980, when he was a cardinal in Germany, Pope Benedict had agreed that a priest accused of abusing a young boy be given therapy rather than the police being brought in to investigate. The priest went on to re-offend but he remained in the Church.

In his pastoral letter to the Catholics of Ireland, read at Masses over the weekend, the Pope apologised for the deep hurt caused to abuse victims and their families.

"You have suffered grievously, and I am truly sorry," he said.

Although the Pope made a full apology to the victims of abuse, his failure to apologise for a systematic cover-up in which accused clergy were transferred to different areas, or the abused sworn to silence, has angered some people.

The high-profile Fermanagh priest, Fr. Brian D'Arcy, himself a child victim of sex abuse, said he was disappointed that the Pope failed to lay out a major reform programme in his pastoral letter.

"Those reforms should include celibacy, canon law and unquestioning authority," he said. "All those questions need to be asked in the reform of the institution. His letter is only one step on the way." Fr. D'Arcy criticised the pontiff for linking a decline in churchgoing to sexual abuse.

"He seems to be linking a decline in faith to this abuse, and that is wholly incorrect," he added.