A powerful storm with gusts of up to 216 kilometres per hour made landfall near the city of Satsumasendai in southwestern Kyushu.
Dozens of people have been injured and a quarter of a million homes have lost power after Typhoon Shanshan hit southwestern Japan.
The typhoon, packing gusts of up to 252 kilometres per hour and bringing torrential rain, made landfall near the city of Satsumasendai on Kyushu island at around 8 a.m. Thursday morning (2300 GMT Wednesday), the Japan Meteorological Agency said.
It warned that up to 60 centimetres (23.6 inches) of rain could fall in Kyushu in 24 hours.
Public broadcaster NHK reported that one person was missing and 39 injured in Kagoshima and Miyazaki prefectures.
Aoi Nishimoto, who lives in Fukuoka, Kyushu's main city, said she had called her family in Miyazaki.
“Our house is fine, but there was a tornado in Miyazaki and the power went out in some places. It is worrying,” the 18-year-old student told the AFP news agency.
A Level 5 emergency warning has been issued for the city of Yufu in Oita Prefecture after the Miyakawa River burst its banks, the Japan Times reported.
The same alert was issued in Usa City, also in Oita Prefecture, due to the possible flooding of the Yakkan River. Level 5 alerts are rarely issued and indicate a life-threatening situation.
Power was cut off to more than 250,000 households in seven prefectures on the island, the Kyushu Electric Power Company said.
The meteorological agency expects Shanshan to move across central and eastern Japan, including the capital Tokyo, in the coming days. Authorities have issued evacuation orders for millions of people.
“The risk of disaster due to heavy rains may increase rapidly in western Japan as Friday approaches,” he warned.
Torrential rains brought by Shanshan have drenched large parts of Japan since Tuesday.
Three members of a family were killed when a landslide buried their home in Gamagori, a city in central Aichi Prefecture, on Tuesday night, local media reported.
Carmaker Toyota has suspended production at all 14 of its factories in Japan as a result of the typhoon, while Nissan and Honda have halted operations at their Kyushu plants.
Japan Airlines and ANA jointly cancelled 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.
Typhoons in the region have been forming closer to shore, intensifying more quickly and lasting longer over land due to climate change, according to a study released last month.
