The 73-year-old Magee has been accused of mishandling complaints against priests in his diocese of Cloyne. The Vatican said today without elaboration that the pope had accepted his resignation.
Before being assigned to Ireland, Magee served as secretary to Popes Paul VI, John Paul I and John Paul II.
Irish government-ordered investigations have documented decades of child abuse and church cover-ups.
In a letter released Saturday by the Vatican, the pope apologised for decades of abuse but took no action against bishops blamed for cover-ups.
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