The approach of Typhoon Shanshan, packing gusts of up to 252 kilometres (157 miles) per hour and bringing widespread heavy rain, prompted auto giant Toyota to suspend production at all 14 of its Japanese factories.
"Typhoon Shanshan is expected to approach southern Kyushu with extremely strong force through Thursday and it may make landfall," Chief Cabinet Secretary Yoshimasa Hayashi told reporters.
"It is expected that violent winds, high waves, and storm surge at levels that many people have never experienced before may occur," said Hayashi, the top government spokesman.
The system has already brought heavy rains to wide areas of Japan, and late Tuesday, a wall of mud, rocks and other debris swept away a house in Gamagori, a city in central Aichi prefecture, with five family members inside.
After all-night recovery efforts, a second woman in her 40s was rescued, but a couple in their 70s and a man in his 30s remained unaccounted for, a Gamagori official told AFP.
Kyushu is home to 12.5 million people.
Southern Kyushu is expected to see 500 millimetres (20 inches) of rain in the 24 hours to Thursday morning, and 600 millimetres in the 24 hours to Friday morning, the Japan Meteorological Agency (JMA) said.
Local governments issued evacuation advisories to 810,000 people in the central Shizuoka prefecture on Honshu because of the rain and to 56,000 others in Kagoshima in Kyushu, the fire and disaster management agency said.
The weather agency may also issue a special heavy rain alert for Kagoshima prefecture later Wednesday, an agency official said in a morning news conference.
"It's necessary for us to be on the highest alert," he said, calling for people to evacuate before any violent storm emerges.
Japan Airlines cancelled 172 domestic flights and six international flights scheduled for Wednesday and Thursday, while ANA nixed 219 domestic flights and four international ones on Wednesday, Thursday and Friday.
The cancellations affected around 25,000 people.
Kyushu Railway said it would suspend some Shinkansen bullet train services between Kumamoto and Kagoshima Chuo from Wednesday night and warned of further possible disruption.
Trains between Tokyo and Fukuoka, the most populous city on Kyushu, may also be cancelled depending on weather conditions this week, other operators said.
Shanshan comes in the wake of Typhoon Ampil, which disrupted hundreds of flights and trains this month.
Despite dumping heavy rain, it caused only minor injuries and damage.
Ampil came days after Tropical Storm Maria brought record rains to northern areas.
Typhoons in the region have been forming closer to coastlines, intensifying more rapidly and lasting longer over land due to climate change, according to a study released last month.
hih-kh/stu/cwl
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