Early in the Meiji period, even the existence of Daigo-ji Temple was threatened due to the Ordinance for Distinguishing Shinto and Buddhism coupled with the Ordinance for the Secularization of Monzeki, Haibutsu-kishaku Movement (a movement to abolish Buddhism) and the Ordinance for Banning Shugendo.
明治初年の神仏分離令以後相次いだ「門跡還俗令、廃仏毀釈、修験道禁止令等」により、醍醐寺の存続すらも危ぶまれるに至った。