There are the Department of Administrative Management (3 divisions with an instructor), the Department of Cultural Heritage (3 sections), the Department of Heijo Palace Site Investigations (6 sections with an instructor), the Department of Asuka/Fujiwara Palace Site Investigations (4 sections), and the Asuka Historical Museum (Curatorial Section) under the Manager.
所長の下に管理部（3課1専門官）、文化遺産研究部（3室）、平城宮跡発掘調査部（6室1専門官）、飛鳥藤原宮跡発掘調査部（4室）、飛鳥資料館（学芸員室）を設置する。