Kangakuin was operated by the Toshi Choja (the chief of the Fujiwara clan) who controlled the appointment and dismissal of individuals to the following posts: Kugyo Betto (the head principal) to which one of the Dainagon (chief councilor of state) of the Fujiwara clan was appointed, Ben no Betto (a second principal) to which members of the Benkan (the Board of Controllers) were appointed, among other officials.
維持管理は藤氏長者の職務とされ、藤原氏一門の大納言級から任じられる公卿別当、弁官から任じられる弁別当以下の職員の任免を行った。