Although, the Suzaku-mon Gate (restored in the Heijo Palace Site) as well as the Excavation Site Exhibition Hall and the Former Imperial Audience Hall (under restoration) belong to Agency for Cultural Affairs, the museum cooperates in administration and research.
平城京跡に復元された朱雀門や遺構展示館、復原工事中の第一次大極殿は文化庁所有だが、管理・研究に協力する。