At his trial in Tralee there were pleas of mercy for him, in particular, and Nunan was sent to Australia for seven years on 8 August 1867. During the voyage Nunan wrote humorously for the ship's newspaper ("The Wild Goose") about his escape from the train and he also organised social events for his fellow convicts. The newspaper was issued and read aloud weekly on board. There were over 250 convicts aboard the "Hougoumont"; more than sixty of these were fellow Irish nationalists. Most of these were there as a result of the March 1867 abortive Fenian Rising. Nunan was taken to the convict establishment in Fremantle where he had to remain until 1869. In May the British Government under William Gladstone decided on a more conciliatory approach to Irish politics and Nunan was amongst those who were pardoned. Nunan could have returned to County Kerry but he elected to remain in Western Australia. He undertook to superintend construction of the new convent building in Victoria Square for the Sisters of Mercy, which had been designed by Richard Roach Jewell. Nunan was already known as an expert in design and he had been approached by Father Patrick Gibney who was the new resident priest in York to build a new larger church for his growing congregation.