In 1846 Bishop Pompallier left for Europe, and following on his report to Pope Pius IX and the Congregation of Propaganda, New Zealand was in 1848 divided into two dioceses, that of Auckland being the province of Auckland, and that of Wellington comprising the rest of New Zealand. Bishop Viard was to remain coadjutor to Pompallier, with his residence in Wellington and be Administrator Apostolic of that diocese.

Hone Heke's rising at Kororareka in 1845 led Pompallier to decide to make Auckland his headquarters, and Bishop Viard dedicated St. Patrick's Cathedral there in March 1848, just two years after he had laid the first stone. When Pompallier returned to New Zealand, in April 1850, he brought to Auckland several French and Irish missionaries, and the first Sisters of Mercy. These were from St. Leo's Convent, Carlow, Ireland, and they began immediately to take over the existing parish schools and founded an orphanage.

Progress in Auckland diocese was hampered through the departure of the Marist missionaries, many of whom accompanied Bishop Viard to Wellington in May 1850 when he left to assume his duties as Administrator Apostolic of the southern diocese. Pompallier's new missionaries faced great difficulties in taking over from the Marist pioneers as they had to learn a new language for the Maori work and meet increasing demands from the growing number of immigrants. Had it not been for the heroic work of Dr James McDonald, all the work of the early missionaries among the Maoris might have been lost.

To recruit more assistants and gain financial help, Bishop Pompallier again visited Europe in 1859, returning in 1860 with fresh helpers, including members of the Franciscan Order who for 10 years did valued work in Auckland diocese, and Suzanne Aubert, later foundress of New Zealand's own Order of Our Lady of Compassion.

By a papal brief of July 1860 Pompallier was made Bishop of Auckland. At the same time Viard was made Bishop of Wellington and ceased to be Pompallier's coadjutor.

Land disputes, followed in 1860 by warfare in Taranaki and later in the Waikato, along with the Hauhau outbreak, caused distrust between Maori and European for many years. The transfer of the capital from Auckland to Wellington, and financial depressions, brought unending problems for Pompallier, who left for Europe in 1868 and resigned his see in 1869. He was made a titular Archbishop in recognition of his valiant work. He retired to Paris where he lived through the Franco-Prussian War, doing much pastoral work until he died on 21 December 1871.