The severe storm hitting central and western Japan has injured at least 31 people and cut power to more than 150,000 homes.
Typhoon Jongdari has brought torrential rain and winds of up to 180km/h (110mph) to areas already hard hit by recent floods and record-breaking heat.
“We have been on emergency alert the whole time since the rain disaster,” said Koji Kunitomi, a crisis management official in the western prefecture of Okayama.
Jongdari made landfall on the country’s main island, Honshu, at 01:00 on Sunday.
Weather officials have since downgraded it to a tropical storm, but warn that heavy rain could trigger landslides.
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150,000 homes are currently without power, reports Japan’s public broadcaster NHK.
As of midday local time, the storm was moving westwards and tens of thousands had been urged to leave their homes.
On Saturday, evacuation orders were issued to 36,400 people in the western city of Shobara, and 6,300 in the city of Kure.
“We are afraid that people may not be able to evacuate due to strong wind or floods blocking evacuation routes,” said Hiroshima’s governor, Hidehiko Yuzaki.
“I would like people to evacuate in advance so that they can save their lives.”
Hundreds of flights were also cancelled over the weekend as the storm neared the coast.
The recent devastating floods were swiftly followed by an unprecedented heatwave which was declared a natural disaster — Japan: Swings from Extremes.