Not strictly speaking - the best selling shooter in Japan was, according to the Game Data Library, Resident Evil 2 which sold 2,456,651 units.
famitsu (games source for game data library)
01 - Splatoon 2 (Nintendo) {2017.07.21} – 2.272.180 + 187.814 digital = 2.459.994
https://www.resetera.com/threads/me...-2018-apr-30-may-06.41349/page-8#post-7742889