The sexual abuse in the Roman Catholic Diocese of Cloyne was investigated by the Commission of Investigation, Dublin Archdiocese, Catholic Diocese of Cloyne, examining how allegations of sexual abuse of children in the diocese were dealt with by the church and state. The investigation was led by Judge Yvonne Murphy, The Cloyne Report, and published in July 2011. The inquiry was ordered to look at child protection practices in the diocese and how it dealt with complaints against 19 priests made from 1996.
In February 2008, the Irish Government referred two allegations of child sex abuse to the National Board for Safeguarding Children, an independent supervisory body established by the Irish bishops, led by Mr Ian Elliott. When the chief executive of that body made contact with the diocese on the matter, he was met with lack of co-operation. Meetings held with Bishop John Magee and representatives of the diocese in March failed to elicit his full co-operation with the National Board for Child Protection's investigation. As per BBC News, "The report found that Bishop John Magee falsely told the government and the health service that his diocese was reporting all abuse allegations to authorities. It also found that the bishop deliberately misled another inquiry and his own advisors by creating two different accounts of a meeting with a priest suspecting of abusing a child, one for the Vatican and the other for diocesan files".
In April 2008, Justine McCarthy, a journalist with the Sunday Tribune, broke the story of the impending scandal in the diocese of Cloyne. There followed a number of hastily arranged meetings between Magee, Monsignor Denis O'Callaghan, (the Vicar General of Cloyne), and Dean Eamon Gould with representatives of the National Board for Safeguarding Children in the Catholic Church (or Safeguarding for short). These resulted in O'Callaghan handing over documentation concerning the two cases referred by the Irish Government to Safeguarding.
On 28 June 2008, Ian Elliott, the chief executive officer of Safeguarding, completed a damning report on the handling of both cases by Magee, by his delegate for Child Protection, O'Callaghan, and by his inter-diocesan case management committee. The Elliot Report was examined by that case management committee on 9 July 2008, and it adopted a position threatening Elliot and Safeguarding with legal action were they to publish the Report. In the meantime, Elliott passed the report to the Irish Government and to the minister for Children, Barry Andrews who did not read the report but passed it to the Health Service Executive to compile another report on it.