Many of the first inmates at the Shujikan tended to have been imprisoned for ideological offenses; these inmates included fuhei shizoku (discontented former samurai) who had been captured during the Seinan War, and in later years, those who had been arrested due to their participation in the Kabasan Incident, the Chichibu Incident, and so on.
当初の受刑者には、西南戦争などで捕縛された不平士族、後年には加波山事件や秩父事件などに参画して逮捕された者など、思想犯的な傾向を持つ収容者も多かった。