After that, until the Edo period, the Kyoogokoku-ji Temple had played a role as the head temple of the Shingon sect, and during the Meiji period, various schools of the Kogi Shingon sect and the Shingi (new) Shingon sect were integrated in accordance with the religious policy of the government.
以降、江戸時代まで、教王護国寺は真言宗の長者寺としてその役割を果たしてきたが、明治時代に入ると、政府の宗教政策から、真言宗は、古義真言宗・新義真言宗各派が合同することとなった。