A July deadline is seen as giving the Bishop a six-month reprieve in which to salvage some of his badly bruised public image, and restore his pastoral authority.
The Government has ordered the new probe by the Dublin Archdiocese Commission of Investigation, after the publication of a HSE audit earlier this week.
It emerged Bishop Magee had misled authorities when he told the HSE he was compliant with child protection guidelines, but had not informed authorities one of his priests was under investigation for abuse claims.
Dr Magee has vowed to co-operate fully with the new inquiry, led by Circuit Court Judge Yvonne Murphy.
But last night, sources close to Bishop Magee said he was determined to remain at the helm of his sprawling Cork diocese. And the Diocese of Cloyne is understood to be planning church events as normal, and no change in administration is envisaged.
Dr Magee is scheduled to commence confirmations of children in Cloyne schools from mid-March, and on February 17 he will mark his 22nd anniversary as Bishop of Cloyne. He is also scheduled to lead the annual diocesan pilgrimage to Lourdes later in the year.
However, informed church sources pointed out that Dr Magee has become an isolated figure from the rest of the Irish bishops, two of whom -- Cardinal Sean Brady, and Archbishop of Dublin Diarmuid Martin -- have signalled their complete dismay at his failure to apply agreed procedures dating back to 1999.
Bishop Magee is also said to have been stunned by an outspoken remark by Bishop John McAreavy of Dromore, in his own homeland of Newry, who called on him "to think about his position".
Reaction
In Cobh yesterday there was mixed reaction to the controversy.
The Mayor of Cobh, Cllr John Mulvihill Jnr, said the HSE study endorsed the earlier NBSC report.
"The main thing is that trust has been broken throughout the Diocese of Cloyne and that has to be restored," he added.
"To be fair, Bishop Magee was not the only one at fault and we must not forget that".
But Cork East Labour TD Sean Sherlock again warned that the bishop should consider his position.
No further comment is expected from Dr Magee on the controversy. He has already apologised and accepted personal responsibility for the manner in which the allegations were handled.
Meanwhile, the Rape Crisis Network of Ireland has voiced no-confidence in the new Government-ordered probe, as long as Bishop John Magee remains in office.
Director of the Rape Crisis Network Fiona Neary said that "the only cooperation that would be required from Bishop Magee is that he step down to allow the new government probe to have credibility".
Ms Neary described the HSE audit as "a failed opportunity to audit the practice of the Catholic Church in relation to child protection".
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(Source: II)