Powerful storm with gusts of up to 216km per hour made landfall near Satsumasendai city in southwestern Kyushu.
Dozens of people have been injured and power was cut to a quarter of a million households after Typhoon Shanshan struck southwestern Japan.
The typhoon, bringing gusts of up to 252 kilometres (157 miles) per hour and torrential rain, made landfall near Satsumasendai city on Kyushu island at about 8am on Thursday morning (23:00 GMT on Wednesday), the Japan Meteorological Agency said.
It warned up to 60 centimetres (23.6 inches) of rain could fall in Kyushu over 24 hours.
Public broadcaster NHK reported one person was missing and 39 injured in Kagoshima and Miyazaki prefectures.
Aoi Nishimoto, who lives in Kyushu’s main city of Fukuoka, said he had called his family back in Miyazaki.
“Our home is fine, but there was a tornado in Miyazaki and power went out in some places. It’s worrying,” the 18-year-old student told the AFP news agency.
A Level 5 emergency warning was issued for the city of Yufu in Oita Prefecture after the Miyakawa River burst its banks, the Japan Times said.
The same warning was in place in the city of Usa, also in Oita Prefecture, because of possible flooding from the Yakkan River. Level 5 alerts are rarely issued and indicate a life-threatening situation.
Power supply was cut to more than 250,000 households across seven prefectures on the island, the Kyushu Electric Power Company said.
The weather agency expects Shanshan to move through Japan’s central and eastern regions, including the capital Tokyo, in the coming days. Officials have issued evacuation orders for millions of people.
“The risk of a disaster due to heavy rain can rapidly escalate in western Japan as Friday approaches,” it warned.
Torrential rain brought by Shanshan has drenched large parts of Japan since Tuesday.
Three members of a family were killed when a landslide buried their house in Gamagori, a city in central Aichi prefecture, late on Tuesday, according to local media.
Carmaker Toyota has suspended production at its 14 factories across Japan as a result of the typhoon, while Nissan and Honda have stopped operations at their Kyushu plants.
Japan Airlines and ANA have together cancelled hundreds of domestic flights that were scheduled for Thursday and Friday. Some rail services have also been affected.
Shanshan is the third major storm system to hit Japan this month.
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.