The typhoon prompted the government to urge residents to watch for landslides and flooding.
The Kyodo news agency reported there has been record rainfall in parts of the Izu island chain located 174 miles south of the Japanese capital.
Hundreds of people took refuge at evacuation centres.
One man died after being swept away by waves while fishing in Oiso in the Kanagawa prefecture, on the main Japanese island of Honshu.
AloJapan.com