The Yomiuri Shimbun says Tokyo has selected Akita and Yamaguchi prefectures for the two Aegis Ashore sites.
By Commander, U.S. Naval Forces Europe-Africa/U.S. 6th Fleet (Aegis Ashore Missile Defense Complex Romania) [Public domain], via Wikimedia Commons
They will be located at Japan Ground Self-Defense Force facilities and manned by soldiers from JGSDF.