There is an irony in the custody of this manuscript that is worth drawing out rather than passing over. The Kojiki is the foundational narrative of the kami, the account of the creation of the islands, of Amaterasu and the rock cave, of the descent of the heavenly grandchild and the line of emperors that follows from it. It is the text on which the modern idea of Shinto as a distinct native tradition was substantially built, particularly by the eighteenth-century scholar Motoori Norinaga, whose commentary took thirty-five years.
The manuscript that carries it was copied by a Buddhist monk, in a Buddhist temple, and has been kept in a Buddhist temple's library ever since. Shinpuku-ji, whose collection it belongs to, was absorbed into Osu Kannon in Nagoya, where it remains, deposited for keeping and study at the Nagoya City Museum and designated a National Treasure.
This is a fair picture of Japanese religious history rather than an anomaly. For most of the period between the Kojiki's compilation and the nineteenth century, kami worship and Buddhism were not separate institutions with separate libraries but a single combined religious system, and it was temples that had the scriptoria, the scholars and the means to keep paper safe for six hundred years. The forced separation of the two in 1868 came long after this copy was made.