clarke accompanied commissioner william spain as an interpreter, during his inquiry into the claims of the new zealand company, and was fiercely assailed by the representatives of the company. eventually the claims of the company were reduced. new plymouth and manawatu were shown to have been purchased correctly but in most other cases the new zealand company had to pay further sums to māori as compensation. in june 1844 clarke was sent to otago to assist in the purchase of a large block of land for the projected scottish settlement. 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. for eight of the early months of 1845 clarke was in the centre of the war with the māori, and for most of the time was the only representative of the government in the district. on 18 november 1845 governor grey arrived and clarke was at once attached to his personal staff. grey was anxious to put an end to the war and eventually peace was declared. 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". in another place he mentions that "heke always said, if fight we must, let us fight like gentlemen". but though clarke could pay these well-deserved tributes in his account of the great chief, he could say little about his own conduct as representative of the government, which was equally creditable. in 1846, greatly to the regret of grey, clarke resigned from the government service. 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.