Whiteley supported the Government during the First and Second Taranaki Wars, conflicts with the Taranaki "iwi" arising from disputed land purchases and religious tensions and which took place in the first half of the 1860s. For part of the war, Whiteley's school, the Grey Institute, was closed but was reinstituted in 1865. During this time, in his sermons to Māori he advocated for them to cease their hostile acts and defer to the Government. In his view, to follow Christianity was to also require allegiance to the Crown and he used scripture to emphasise this. He also reported back to the authorities, providing intelligence on the areas and people he visited while on his ministrations. The WMS and his fellow missionaries felt that Whiteley should be more circumspect in advancing his views, with some expressing concern for his safety. Despite this, he continued to keep up his practice of travelling around the region to preach at Māori villages.