The Nihon Shoki records the founding of the Kudara Dai-ji (百済大寺), predecessor of the Daian-ji, in 639 during the reign of Emperor Jomei. A nine-story pagoda was added shortly afterwards. Moved during the reign of Emperor Tenmu, excavations have uncovered the foundations of the site of the Daikandai-ji (大官大寺), as it was then known, seven hundred metres to the south of Mount Kagu. Like the Yakushi-ji, and Gangō-ji, the temple relocated to the new capital of Heijō-kyō in 716–17, and it was rebuilt as the Daian-ji in 729. Its importance declined when the capital moved again to Kyoto at the end of the Nara period. A succession of fires, a typhoon in 1459 and earthquakes in 1585 and 1596 destroyed most of the temple. The stone bases of the former twin pagodas were removed for reuse at Kashihara Jingū in 1889, while the ruins of the other buildings lie in adjacent properties.