Following the North-West Resistance in 1885, the administration of Rev. Thomas Clarke was frequently criticized for the school's inadequate diet and lack of medical attention given to the students. Clarke attempted to deflect the blame for insufficient food onto the Department of Indian Affairs, claiming "there is not a meal without the children asking for more bread. In Spite of Macrae's orders, I have given it to them." Clarke rejected the complaints about the students receiving poor medical attention as untrue, reporting in 1887 that "the health of the boys had been very good except for common minor ailments." The Indian Agent at Carlton reported that the children’s parents frequently complained about their children’s treatment and the fact that the sick were not looked after properly. For example, children were insufficiently fed, poorly clothed, and dirty and were isolated and neglected in the sick ward when ill. They also said that the children were improperly supervised giving the older children opportunity to bully and mistreat the younger children. - These reports were substantiated by "Indians whom I have generally found worthy of credence.." according to the Indian Agent. These complaints, combined with a dwindling attendance rate and criticisms of his management of the school staff, led to Rev. Clarke being fired from his position as principle of the Battleford Industrial school in 1894.
(McCord Museum, Reed Family Papers, Box 1, Folder 6, T. Clarke to H. Reed, 28 Sept. 1891.) (Reed Papers, vol. 16, file Battleford 1897-92, 479, Finlayson to H. Reed, 12 June 1891, 'Private'.)