Archbishop Diarmuid Martin has said he is extremely concerned at fallout from the Cloyne clerical child abuse investigation.
He said he is particularly worried that there may be wide diversity in how sections of the church are interpreting and applying agreed national child protection procedures.
He has told his fellow-bishops that if serious doubts were to persist on this question, he would have to implement his own system of accountable child protection.
The Archbishop issued a statement on the matter earlier today, the first comment by a senior churchman since Friday's revelations.
The Church's National Board for Protecting Children found that the east Cork diocese was inadequate and in some respects dangerous in protecting children from sexual abuse.
Dr Martin notes that the Board now feels that Cloyne diocese is fully co-operating in adequately implementing agreed protection procedures.
It is a dozen years since the Church advised its bishops to protect children by reporting allegations of child sexual abuse to the gardaí and health authorities.
Earlier, one of the Government's Special Rapporteurs for Child Protection, Geoffrey Shannon, has called on the Bishop of Cloyne, Dr John Magee, to resign.
Speaking on RTÉ Radio’s News at One, Mr Shannon said it was time to come of the fence. He said it was a time for action and that Bishop John Magee's position was untenable.
Meanwhile Minister for Children Barry Andrews defended his handling of a report that criticised how complaints of child sexual abuse in the Diocese of Cloyne were dealt with.
The minister received the report earlier this year, but passed it on to the Health Service Executive without reading it.
Minister Andrews said Dr Magee must reflect on the findings of the report.
On RTÉ Radio’s Morning Ireland, Mr Andrews said he had dealt with the report in the manner set out by guidelines.
He said he believed he had done the right thing in passing the report straight to the HSE when he received it last year, and he would do the same with any other report.
Yesterday, Mr Andrews said the report on the handling by the Cloyne diocese of abuse allegations was very worrying, and he said he did have concern that the Bishop of Cloyne was patron of all national schools in the diocese which covers 46 parishes in Co Cork.
However, Dr Magee rejected calls to step down.
Also speaking yesterday, the father of an alleged victim of clerical child sexual abuse called for the Church to 'kick out' Dr Magee. He said the bishop should account for himself before being fired.
It follows a report by the National Safeguarding Board for Children in the Catholic Church (NBSCCC), published last week, which found the Catholic Church had not responded properly to abuse allegations.
A NBSCCC review of child abuse inquiries in the Diocese of Cloyne found that Church authorities broke their own rules on reporting allegations.
A schoolgirl's allegation, as well as four similar allegations, was not reported by the diocese to the gardaí.