Typhoon Shanshan, Japan's strongest storm of the year, made landfall on the island of Kyushu at around 8 am on August 29.
The typhoon brought torrential rain and winds of up to 252 km/h.
Many structures have suffered damages and over 250,000 households lost power. Transport and flights were cancelled, and tens of thousands were advised to evacuate.
A rare special warning for violent storms, waves and high tides was issued for most of Kagoshima, with residents urged to stay on high alert.
Reports of deaths in landslides have emerged, with three members of a family killed in Gamagori.
Heavy rains are expected to continue across much of the nation, even in areas far from the storm.