On March 14, 1782, he received the appointment of Superintendent General and Inspector General of Indian affairs from Sir Frederick Haldimand, due to the dismissal of his cousin Guy Johnson. In 1781, General MacLean reported that Guy Johnson's wartime accounts were "Extravagant, wonderful & fictitious, and the quality of articles so extraordinary, new & uncommon". Guy Johnson was suspended as superintendent and summoned to Montreal, where Haldimand criticized his conduct as "reprehensible". Guy Johnson was disgraced and departed for London to defend his reports to the government, but met with no success. Sir John took over Fort Niagara as superintendent of Indian affairs in his cousin's absence, later to be appointed in full. The authority of the position extended over all northern First Nations allied with the Crown, including four of the Iroquois League nations, most of whom had relocated to Canada after having been allies of the British during the revolution.