The arrangement was ended by order of an occupying army. On 15 December 1945 the Supreme Commander for the Allied Powers issued the Shinto Directive, abolishing state sponsorship, support, control and dissemination of what it called State Shinto. The directive did not ban Shinto. It reclassified it as a religion, cut it off from public funding and from the state administration that had run it, and prohibited its use as an instrument of ideology. Disestablishment, not prohibition.
The shrines then had to organise themselves, and in February 1946 they founded the Association of Shinto Shrines, a single religious corporation with an office in every prefecture. Something on the order of seventy-eight to seventy-nine thousand shrines belong to it, out of roughly a hundred thousand in the country. Member shrines take the Ise Grand Shrine as the foundation of their practice, and the association distributes Ise's Jingu Taima amulets, a system that is both the doctrinal and the financial spine of the arrangement. It runs two universities for the training of priests.
Not everything belongs to it. Fushimi Inari Taisha and Nikko Toshogu are independent, and so is Yasukuni. A steady sequence of prominent shrines has left in recent decades over governance, autonomy and money: Meiji Jingu withdrew in 2004 and rejoined in 2010, Tomioka Hachimangu left in 2017, Kotohira-gu in 2020, Kamakura-gu in 2024.
The association also has a political arm, which lobbies on national symbols, on education, and on official visits to Yasukuni. Whether that is compatible with the constitution's separation of religion and state is argued in Japanese politics continually.