In 1860-61, Wilson was a missionary-chaplain to Māori war-parties at the Otawhao Mission of John Morgan and at Waitara, Taranaki. He acted as chaplain with permission of the commanders of the colonial government forces but he did not have the permission of Bishop Selwyn. He was present at the Battle of Puketakauere on 23 June 1860; the action at Huirangi in December 1860 against the major Māori defensive line called Te Arei that barred the way to the historic hill pā of Pukerangiora; and the battle on 23 January 1861, when the Māori warriors attacked a redoubt, which was garrisoned by the 40th Regiment.