In December 2008, Magee was at the centre of a controversy concerning his handling of child sex abuse cases by clergy in the diocese of Cloyne. Calls for his resignation followed. On 7 March 2009, Magee announced that, at his request, the Pope had placed the running of the diocese in the hands of Dermot Clifford, metropolitan archbishop of the Archdiocese of Cashel and Emly, to whose ecclesiastical province the diocese of Cloyne belongs. Magee remained Bishop of Cloyne, but withdrew from administration in order, he said, to dedicate his full-time to the matter of the inquiry. On 24 March 2010, the Holy See announced that Magee had formally resigned from his duties as Bishop of Cloyne and was now bishop emeritus.