Cardinal Sean Brady said the bishop should stay to ensure proper procedures were put in place.
The cardinal did not believe that Bishop Magee should resign over his mishandling of allegations against two priests, but should be held accountable to a new State probe into child protection procedures in his diocese.
Cardinal Brady's unexpected support appeared to have the approval of the Vatican, and it provided a major boost for the besieged bishop, who has also been given the blessing of five other bishops, including the Archbishop of Cashel, and Dermot Clifford, who is the leader of the Munster Church.
There was no immediate public reaction from Archbishop of Dublin Diarmuid Martin -- the most senior churchman in the Republic -- who last week made his dissatisfaction with the conduct of Bishop Magee clear when he welcomed an Augustinian monk at the Pro-Cathedral after a 'walk of atonement' from Cloyne in support of the victims.
The Cardinal's endorsement of Bishop Magee's ability to introduce proper child protection procedures also brought him into direct conflict with Minister for Children Barry Andrews, who has publicly stated his lack of confidence in the bishop as Patron of Catholic Schools in the diocese, and has called on him several times to consider his position.
Last night, the victims' support group, One in Four, stood firmly behind its earlier calls for Bishop Magee's resignation, and it appealed to the Government to step in and ensure that children were protected in Cloyne.
"If the Church authorities are refusing to take responsibility, we call on the minister to step in and ensure that children are protected in Cloyne," One in Four Director Maeve Lewis said.
The renewed tensions in Church-State relations resurfaced suddenly yesterday at lunchtime when Cardinal Brady spoke to RTE.
The Cardinal said he was sure that public trust had been damaged by the revelations that Bishop Magee had been found by an internal church inquiry to have applied child safeguard procedures that were "inadequate and dangerous".
Cardinal Brady said he accepted that people were angry at the serious issues raised in Cloyne and that there had been many calls for Bishop Magee's resignation, but that the first question must always be the suffering of victims.
Reflection
"On reflection I think he should not resign," the Cardinal said.
"He has begun to address these serious issues. He has introduced new procedures. He has accepted responsibility for them and he has apologised."
Cardinal Brady said he had known the former secretary to three Popes for 50 years, and knew him to be "dependable and reliable". He believed Bishop Magee (72) had learned a very painful lesson.
"There is no pastoral issue more critical for the Church in Ireland today than to ensure the right attitudes and the right procedures are in place to safeguard children," said the Cardinal.
But last night, Executive Director Maeve Lewis of the One in Four victims' counselling group told the Irish Independent that she was "astounded and disappointed at the Cardinal's turn-around from his position of two weeks ago".
Ms Lewis said that the Cardinal's comments showed a complete lack of understanding of the dynamics of sexual abuse.
"While he acknowledges the suffering of victims, he certainly is not taking victims' views into account in this matter," she said.
Ms Lewis added that she had absolutely no confidence in Bishop Magee's ability.
"Just as in the case of Ferns and Dublin, a new, uncompromised leadership is required in the Diocese of Cloyne."
There was also angry reaction last night to the Cardinal's defence of Bishop Magee from the lay Catholic group, the Voice of the Faithful, with Sean O'Conaill, the body's coordinator, saying he was shocked by the Cardinal's intervention.
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(Source: II)