The Bishop began his mission at Hokianga but in 1839 transferred his headquarters to Kororareka. With the arrival of more missionaries from France he began to extend his work, visiting in 1840 even distant Otago. By 1844 he had founded stations at Whangaroa, Tauranga, Rotorua, Matamata, Whakatane, Opotiki, Kaipara, Auckland, Wellington, and Akaroa. At Auckland and Kororareka he established schools for both Maoris and Europeans, the one at Auckland, opened in 1841, being the first in the town. In 1841–42 he visited Wallis, Futuna, Fiji, and Tonga.

After Waitangi, and the establishment of British sovereignty in 1840, the increasing number of settlers and their demands for ministrations created great difficulties. The area which Western Oceania embraced was too vast for fruitful administration and in 1842 Rome made New Zealand an independent vicariate. The rest of the area was named Central Oceania and placed under Bishop Bataillon as Vicar Apostolic. He was given as coadjutor Bishop William Douarre, of the Society of Mary, who made New Caledonia the centre for his work. Douarre received as one of his temporary staff Father Philip Viard, S.M., who had come to New Zealand in 1839 where he was stationed at Russell, Tauranga, and, later, at Wallis Island. Bishop Pompallier recalled Viard from New Caledonia as he wished to have him as his coadjutor. Arriving in Sydney in October 1845 Viard received from his bishop the news of his appointment, and the following January was consecrated by Archbishop Polding, returning to New Zealand with Pompallier a few days later.