After the Meiji period, in accordance with the religious policies of the government, the Koyasan Shingon sect became a part of the Old Shingon sect, which was merged with the other religious schools of the Shingon sect (Omuro school of the Shingon sect [the grand head temple is Ninna-ji Temple], Daikaku-ji school of the Shingon sect [the head temple is Daikaku-ji Temple], etc.), and became the grand head temple of the Old Shingon sect.
明治以降、政府の宗教政策から、他の真言宗宗派（真言宗御室派（総本山仁和寺）・真言宗大覚寺派（大本山大覚寺）など）と合同した古義真言宗に属し、古義真言宗総本山となる。