A tropical storm hit south-western Japan with heavy rainfall and strong winds on Monday, killing at least two people and injuring at least 82 as it headed north towards Tokyo.
More than 340,000 homes are without power, the government said. Officials say more flooding is expected.
Residential streets were inundated with muddy water from rivers, and many homes lost power after Typhoon Nanmadol made landfall on the island of Kyushu on Sunday and then weakened to a tropical storm.
Japanese media reported a man had been found dead in his submerged car, while many people were injured by flying glass amid high winds. Another man had been killed in a landslide and a third person has been reported missing.
Up to 400 mm of rain was expected in central Japan's Tokai region, the nation's industrial heartland, over the next 24 hours, the Japan Meteorological Agency said.
Nanmadol winds were measured at 108 kilometres an hour, with 162 kph gusts, the agency said.
Kyushu Railway Company said it had halted operations on Kyushu and Japan Airlines and ANA Holdings cancelled about 800 flights, public broadcaster NHK reported.
Prime Minister Fumio Kishida delayed his departure to New York, where he is due to deliver a speech at the UN General Assembly, until Tuesday to monitor the impact of the storm, local media reported.
"We need to remain highly vigilant for heavy rains, gales, high waves and storm surges," a JMA official told a news conference.
Tens of thousands of people spent the night at gymnasiums and other facilities in a precautionary evacuation of vulnerable homes.
Torrential winds smashed signboards. A construction crane snapped and other damage was caused in Kagoshima city.
Bullet trains and airlines suspended services. Warnings were issued about landslides and swelling rivers. Convenience stores shut and delivery services were suspended, while some highways were closed. Some people experienced problems with mobile phone connections.
The storm is forecast to continue its north-easterly path over Japan’s main island of Honshu, unleashing heavy rainfall over the region that includes the cities of Osaka and Kyoto, before moving over Tokyo on Tuesday.