[citation needed] He served as a missionary priest in Nigeria for almost six years before being appointed Procurator General of St Patrick's Society in Rome.

On 28 April 1981 Magee travelled, without the knowledge or approval of the Vatican's Secretariat of State, to Long Kesh Prison outside Belfast, Northern Ireland, to meet with IRA hunger striker Bobby Sands.

[4] On 25 July 2006, Magee published a pastoral letter stating: "As a result of An Bord Pleanála's decision, the situation concerning the temporary plywood altar still remains unresolved and needs to be addressed.

The Diocese will initiate discussions with the planning authorities in an attempt to find a solution, which would be acceptable from both the liturgical and heritage points of view.

A February 2006 article by Kieron Wood in The Sunday Business Post claimed that Magee did not have the backing of the Vatican in his proposals for St Colman's.

At the oral hearing of An Bord Pleanála he was requested to provide a copy of the letter from the Vatican in which he claimed he had been given approval for the modernising of Cobh Cathedral.

158/99/L) to the team of architects who worked on the cathedral project from Cardinal Francis Arinze, Prefect of the Congregation for Divine Worship and the Discipline of the Sacraments.

[6] At a meeting of his liturgical advisers and diocesan clergy in November 2006, Bishop Magee spoke of his conversation with the Pope in the course of that ad limina visit at the end of the previous month.

Bishop Magee's contribution to the ad limina visit concerned not only his diocese of Cloyne but also ceremonial matters (an area of expertise for him) on behalf of the Conference.

He also facilitated the broadcasting, in coincidence with the visit, of a life of Pope John Paul I prepared some months earlier by Italian state television (RAI).

In an interview published on the Italian Catholic daily Avvenire on 26 October 2006, Cardinal Secretary of State Tarcisio Bertone criticised the image that the programme presented of Pope John Paul I.

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.

[8][9] The inquiry into Cloyne – the fourth examination of clerical abuse in the Church in Ireland – found the greatest flaw in the diocese was repeated failure to report all complaints.

The French left-wing clerical review Golias reported that the Irishman was in the running to succeed as head of the Congregation for Divine Worship and the Discipline of the Sacraments.

The review suggested that Magee's support for the Latin Mass had won him the Pope's approval, and it said that the bishop's apparent lack of ambition and shyness eminently qualified him for a position in the Vatican.