Magee involved himself in a dispute with the Friends of St Colman's Cathedral, a local conservationist group in Cobh which organised an effective and professional opposition to the Bishop's plans to re-order the interior of Cobh Cathedral, plans similar to previous re-orderings in Killarney, Cork and Limerick cathedrals. In an oral hearing conducted by An Bord Pleanála, the Irish Planning Board, it emerged that irregularities had occurred in the planning application that were traced to Cobh Town Council, which accommodated the Bishop's plans to modify the Victorian interior designed by E W Pugin and George Ashlin. On 2 June 2006, when Bishop Magee was in Lourdes, An Bord Pleanála directed Cobh Town Council to refuse the Bishop's application.