Typhoon Nangka barreled across the western end of Japan's largest main island on Friday, snarling transport, leaving at least two men dead and prompting authorities to advise nearly 100,000 people to evacuate.
Rivers burst their banks in the western prefecture of Wakayama after some parts of Honshu, Japan's largest main island, received more than 600 mm (23 inches) of rain since the storm began to near the island Thursday.
Two men drowned, one of them a 71-year-old man who fell into a flooded ditch while repairing a window, NHK national television said. More than 30 people were injured.
Nangka, named for a tropical fruit, had been downgraded to a tropical storm by Friday morning but still packed sustained winds of 80 kph (51 mph), with gusts of up to 120 kph(75 mph) an hour.
More rain forecast
It was expected to dump a further 300 mm (11 inches) of rain on parts of Japan by Saturday morning.
Authorities advised nearly 100,000 people to evacuate across a wide swathe of western Japan due to the threat of flooding and landslides.
At one point on Thursday, nearly 400,000 people were advised to leave their homes.
Nearly 200 flights were canceled, trains in western Japan suffered delays and highways near the ocean were closed.
The storm is expected to head into the Sea of Japan later Friday and weaken into a tropical depression, then head northeast across the northern tip of Honshu on Sunday.