Typhoon Shanshan slammed into Japan's main southern island of Kyushu early Thursday, with authorities advising thousands of people to evacuate and issuing the highest warning level for wind and storm surges.
The weather office said that Japan's most powerful typhoon this year made landfall at around 8:00 am (2300 GMT Wednesday) packing gusts of up to 252 kilometres (157 miles) per hour.
Kyushu's utility operator said that 254,610 houses were already without power.
"Special warnings of violent storms, high waves and high tides are being issued to the Kagoshima region (of Kyuhsu)," the Japan Meteorological Office said.
"Please exercise maximum vigilance against violent storms, high waves and high tides in Kagoshima, as well as landslides, flooding in low-lying areas and overflowing rivers in southern Kyushu," it said.
"Please also be advised that the risk of a disaster due to heavy rain can rapidly escalate in western Japan as Friday approaches."
Heavy rain brought by Shanshan has been lashing large parts of Japan since Tuesday.
Three members of a family died after a landslide buried a house in Gamagori, a city in central Aichi prefecture, Japan's Kyodo news agency reported early Thursday, citing local government officials.
The deceased included a couple in their 70s as well as a son in his 30s, while two adult daughters in their 40s survived with injuries, Kyodo reported.
For southern Kyushu, the JMA predicted an enormous 1,100 millimetres (43 inches) of precipitation in the 48 hours to Friday morning.
Video on public broadcaster NHK TV showed roof tiles being blown off houses, broken windows and felled trees.
"Our carport roof was blown away in its entirety. I wasn't at home when it happened, but my kids say they felt the shaking so strong they thought an earthquake happened," a local resident in Miyazaki told NHK.
"I was surprised. It was completely beyond our imagination," she said.
Auto giant Toyota has suspended production at all 14 of its factories in Japan.
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.
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