Minister for Children Barry Andrews is to refer the Catholic Diocese of Cloyne to a commission investigating clerical abuse in the Dublin archdiocese.
Mr Andrews was speaking at a press conference to mark the publication of a Health Service Executive (HSE) audit which examined the child-protection policies and protocols in every Catholic diocese in the State.
The audit, which was based on a questionnaire, includes detailed information on complaints and allegations of child sexual abuse against members of the clergy. The Minister said he had decided to refer Cloyne to the commission even though the audit concluded that there was no need to refer any diocese.
"I am not satisfied that Cloyne is operating procedures to the highest standards," said Mr Andrews. He added that the decision to refer Cloyne had been his political decision.
The audit raised concerns about the adequacy of child-protection in a number of dioceses, but particularly in Cloyne.
Mr Andrews said that he had based his decision on the fact that at the time the audit questionnaire was completed, the diocese was handling a complaint in relation to child abuse, which it had failed to notify to the HSE.
"I believe that there is evidence that points to the fact that Bishop [John] Magee, as the responsible person, did not faithfully report actual compliance with child protection procedures and the manner in which clerical sexual abuse allegations have been dealt with," said Mr Andrews.
"Accordingly, the Government has taken the decision to notify the Cloyne Diocese to the Commission of Investigation into the Dublin Archdiocese to carry out an examination of the Diocese (of Cloyne).
Cloyne, which covers most of rural Co Cork, has already been the subject of a separate report which criticised its handling of abuse allegations levelled against members of the clergy. The report was conducted by the National Board for Safeguarding Children in the Catholic Church in Ireland (NBSC), a body set up by, but independent of the Catholic Church.
Mr Andrews said the NBSC had made "damning" findings about the handling of sexual abuse allegations within Cloyne.
"It used very stark language about the way which the diocese operated child-protected procedures including saying that they had operated somewhat dangerous procedures, that they favoured perpetrators over victims in
certain circumstances and had taken a fairly minimalistic role in terms of sharing information with the Board, even as recently as last year.
"In a post-Ferns situation, I took the decision that based on the report of the HSE and the national boards that it was an appropriate set of circumstances to refer to the Commission," he said.
Mr Andrews said that his office would be engaging with both other bodies with to view to finding a mechanism within three weeks that would allow for a proper review of child protection practices in every parish in the country.
"There were legal reasons that were legitimately raised by all parties, not just the church, about the sharing of information that would otherwise be confidential.
"We have come close to an agreement. I am confident that we will come to a methodology within the next few weeks.
"If you look at the quality of the work that the NBSC has done in Cloyne, it would be madness of us not to form a partnership with us, and the HSE."
The Bishop of Cloyne John Magee recently apologised to victims of clerical sex abuse after the report found his diocese had put children at risk of harm through an "inability" to respond appropriately to abuse allegations. The Bishop has faced a large number of calls for his resignation but has signalled his intention to remain.
When asked if Bishop Magee should resign in light of today's reports and the ongoing controversy, Mr Andrew said that there were certain question-marks about his position.
"It remains my position that he does have to reflect on the very serious consequences of the failures that have very patently taken place within his diocese," he said.
"It's a matter for the church whether he retains his positions and a matter for himself personally."
Mr Andrews said he was very disappointed with Bishop Magee. "I am very disappointed. A lot of good people in his diocese are disappointed as is evidenced by the support for Fr Michael Mernagh who walked from Cobh [to Dublin]."
According to the audit, all dioceses stated that they operated a child protection policy and furnished copies of their policies to the HSE.
The audit said that a number of issues were raised by bishops regarding procedures for reporting possible cases of clerical abuse to the HSE and gardaí.
All bishops affirmed that cases of possible or known abuse are notified "without delay". Furthermore, each diocese reported that they have a designated person to whom allegations or suspicions of child sexual abuse are reported and that written records were kept.
Bishops also affirmed that were reasonable grounds exist, action is taken to protect children from possible abuse by an alleged perpetrator.
The audit notes that the majority of dioceses said they had a child protection training programme in place but the HSE stated that it was "disappointing" that a minority of dioceses had not such programmes.
The audit reported that the historical managerial division or autonomy of dioceses entails the HSE to conduct separate audit questionnaires essentially means that a bishop may be unaware that reports of suspected child abuse have been made to the executive or gardaí. It recommended that the church authorities should address this issue.
The Diocese of Cloyne today said it accepted the findings of the HSE report into the management of child sexual abuse issues in the diocese.
"As also outlined in the report the diocese has already appointed a new Child Protection Delegate, accepted in full the recommendations of the National Board for Safeguarding Children (NBSC) and reached agreement with the HSE as regards the need for ongoing collaboration with the HSE in refining child protection practices," the statement from the Diocese said.
It also noted Mr Andrews' decision to refer the diocese to the commission, with Bishop John Magee pledging to give "every possible cooperation" and apologising once more to those who were abused by priests of the diocese.