In a strongly-worded statement, Cardinal Sean Brady pledged a root-and-branch reform of all 26 dioceses, as he desperately sought to restore public confidence in the Church's ability to protect children.
Cardinal Brady announced he would personally require every bishop, congregation and missionary society in the country to give a written commitment to carry out all statutory guidelines to protect children.
He also went as far as suggesting the Church board for safeguarding children should conduct a fresh review of practices in each diocese, in co-operation with the HSE.
The Primate of All Ireland and Archbishop of Armagh admitted recent findings from a damning report on clerical sexual abuse in the diocese of Cloyne had "brought into question" the efforts of thousands of volunteers and trained personnel to protect children.
Cardinal Brady's dramatic intervention, understood by the Irish Independent to have been issued after consultation with Pope Benedict, brings him out on the side of the Archbishop of Dublin, Diarmuid Martin, who had threatened to withdraw co-operation from fellow bishops, including Bishop Magee.
Last night, church sources predicted that if Bishop Magee, a former secretary to three popes, did not stand down before the Cabinet meets next Wednesday, Rome might be forced to remove him.
A spokesman for Bishop Magee last night said he had "nothing further to say" about his position, but added: "The (child protection) board has and will continue to have the full cooperation of the Bishop and the diocese in its important work."
Children's Minister Barry Andrews last night welcomed Cardinal Brady's statement, in particular "his specific comments in relation to Cloyne".
However, abuse charity One-in-Four last night said Archbishop Brady's intervention was "too little, too late".
Executive Director Maeve Lewis called on the Bishop of Cloyne to stand down and criticised Cardinal Brady for failing to comment directly on his handling of the scandal.
Campaigning priest Fr Michael Mernagh, who last night continued to lead a protest march from Dr Magee's seat at St Colman's Cathedral in Cobh to the Pro Cathedral in Dublin, said a review of the guidelines should have been carried out "long ago".
The Cardinal's statement stressed his full confidence in the National Board for Safeguarding Children in the Catholic Church, which first probed Cloyne, and called on it to issue its first annual report.
Last night, the Primate broke his two-week silence since publication of the board's damning report on the diocese, which found its child protection practices were inadequate and dangerous.
The crisis takes on added significance with the imminent publication of the report of a Government Commission of Inquiry into the country's biggest diocese, Dublin.
It is expected that the report will contain some shocking revelations, that could rock Church and State to their very foundations.
The Vatican has, to date, not publicly commented on the controversy.
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