As for the Honzon Yakushi Sanzonzo in the Kon-do Hall, attaching importance to the description in "Nihonshoki" of 'Mushadaie Festival was held at Yakushi-ji Temple in 688,' a theory suggests that those statues had already been produced by 688, and then they were later moved to Yakushi-ji Temple at Heijo-kyo.
金堂本尊薬師三尊像については、『日本書紀』に見える、「持統天皇2年（688年）、薬師寺にて無遮大会（むしゃだいえ）が行われた」との記述を重視し、この年までには造立されて、後に平城薬師寺に移されたとする説がある。