In 1839 he went with Williams to Poverty Bay,[4] still continuing his studies, and there obtained an excellent knowledge of the Māori language, and of the mentality of the Maoris; an invaluable experience that he found of great use a year or two later.
Clarke had already formed the ambition of becoming a clergyman, but for five years he remained in the government employ, first as an interpreter, then as a Maori advocate and protector, and eventually as a negotiator with the Māori .
Clarke had to fight hard to preserve the Māori pā, village cultivations and burial grounds, but eventually succeeded, and the sale of something over 400,000 acres (1,600 km²) of what is now the province of Otago was concluded.
Clarke wrote out the original Māori deed and English translation, and took pride in the fact that no dispute ever arose subsequently in regard to the transaction.
Clarke said of this conflict "Heke's war stands quite alone in the history of our struggles with the Maori race; alone in its magnanimity, its chivalry, its courtesy, and, I dare say, its control by Christian sentiment".
Grey pointed out to him that he had splendid prospects if he would remain, but his health had suffered, he still retained his ambition to be a minister of the Gospel, and, moreover, he could not reconcile his conscience with some of the acts of the government.
Soon a larger church was built in Davey Street, and for over 50 years he remained its pastor, honoured and beloved by all and never losing his appeal to the younger people.
Apart from his Notes on Early Life in New Zealand, which appeared in 1903, Clarke's only publications were some separately published sermons and addresses and a small collection of Short Liturgies for Congregational Worship.