A violent storm with gusts of up to 216 km/h reached the mainland near the city of Satsumasendai in southwest Kyushu.
Dozens of people were injured and a quarter of a million households were left without electricity after Typhoon Shanshan hit southwest Japan.
The typhoon, which brought gusts of up to 252 kilometers per hour and torrential rain, made landfall near the city of Satsumasendai on the island of Kyushu at around 8 a.m. Thursday morning (11 p.m. GMT Wednesday), the Japan Meteorological Agency said.
It was warned that up to 60 centimeters (23.6 inches) of rain could fall in Kyushu within 24 hours.
Public broadcaster NHK reported that one person was missing and 39 injured in Kagoshima and Miyazaki prefectures.
Aoi Nishimoto, who lives in Kyushu’s capital Fukuoka, said he called his family in Miyazaki.
“Our home is fine, but there was a tornado in Miyazaki and there were power outages in some places. This is worrying,” the 18-year-old student told AFP news agency.
A level 5 emergency warning was issued for the city of Yufu in Oita Prefecture after the Miyakawa River overflowed its banks, the Japan Times reported.
The same warning was issued in the city of Usa, also in Oita Prefecture, due to possible flooding from the Yakkan River. Alert level 5 is rarely issued and indicates a life-threatening situation.
According to the Kyushu Electric Power Company, power was cut off to more than 250,000 households in seven prefectures on the island.
The weather agency expects Shanshan to move through central and eastern Japan, including the capital Tokyo, in the coming days. Authorities have issued evacuation orders for millions of people.
“The risk of a disaster due to heavy rain may escalate rapidly in western Japan as Friday approaches,” she warned.
Since Tuesday, Shanshan National Park has flooded large parts of Japan with torrential rain.
Three members of a family were killed when a landslide buried their house in Gamagori, a city in central Aichi Prefecture, late Tuesday, local media reported.
Automaker Toyota has suspended production at its 14 factories across Japan as a result of the typhoon, while Nissan and Honda have suspended operations at their plants in Kyushu.
Japan Airlines and ANA jointly canceled hundreds of domestic flights scheduled for Thursday and Friday. Some rail services were also affected.
Shanshan is the third major storm system to hit Japan this month.
According to a study published last month, climate change is causing typhoons in the region to form closer to the coast, intensify more quickly and stay over land longer.
