However, Kyobusho could not achieve significant results because of the critical conflict between the up-and-coming Shintoism group and the Jodo Shinshu Buddhist sect group that had kept its long-established power, and eventually the Jodo Shinshu sect broke away from Daikyoin, which led to the abolition of Kyobusho on January 11, 1877 while its functions were transferred to the Bureau of shrines and temples.
しかしながら、当時新進であった神道勢力と旧来よりの勢力を保っていた浄土真宗との深刻な意見対立によって実績は揚がらぬまま、浄土真宗の大教院離脱を経て、明治10年（1877年）1月11日に廃止、機能は社寺局へ移された。