Five million people have been urged to evacuate and thousands of households are without power. The torrential rains and strong winds have caused several deaths and extensive damage to infrastructure.
Around 80 people are injured, most of them with minor injuries from shattered glass when the typhoon's winds blew in windows and tore tiles off rooftops on Kyushu, the southernmost of Japan's four main islands.
Floods have simultaneously caused chaos in traffic, with blocked roads and warnings of landslides. Hundreds of domestic flights have been cancelled, as well as the high-speed train Shinkansen between Tokyo and Osaka.
Climate change has led to typhoons forming closer to the region's coastlines and intensifying faster, according to a study published in July.