Typhoon No. 4 brought pounding rain to large areas as it traversed the nation before transforming into an extratropical cyclone, The Yomiuri Shimbun reported Thursday.
The storm forced the cancellation of some 83 flights Wednesday and disrupted cellular phone service in parts of Tokyo and seven prefectures.
Flooding was reported in a number of prefectures.
The typhoon prompted evacuation advisories in quake-hit areas of the Tohoku region.
A 16-year-old girl went missing in the Kurosawagawa river in Yamanashi prefecture where a search for her continued.
Temperatures topped 86 degrees in central Tokyo following the typhoon, the Japan Meteorological Agency said.