At least 47 people were missing and five were in a critical condition as torrential rain that has killed 27 people pounds western and central Japan, public broadcaster NHK said on Saturday.
It reported that more than 1.6 million people had been evacuated from their homes.
Japanâ€™s Meteorological Agency issued special weather warnings across four prefectures in the west of Japanâ€™s main island of Honshu, urging vigilance against landslides, rising rivers and strong winds amid what it called â€œhistoricâ€ rains.
In Motoyama, a town on Shikoku island about 600 km from Tokyo, 583 millimetres (23 inches) of rain fell between Friday and Saturday mornings, the Meteorological Agency said.
The agency said that although a weather front had settled between western and eastern Japan, there was a risk that heavy rains would continue as warm air flowed towards the front. Already-saturated areas faced more rain on Sunday, it said.
Among the dead were a man who fell from a bridge into a river in the western city of Hiroshima, and a 77-year-old man in Takashima, about 56 kilometres east of Kyoto, who was swept into a canal as he worked to remove debris, NHK said.
Five other people in Ehime, Hiroshima and Yamaguchi prefectures were in critical condition after being injured in landslides, the broadcaster said.
By Saturday morning, more than 1.6 million people had been ordered to evacuate their homes for fear of flooding and further landslides, with 3.1 million more advised to leave, the Fire and Disaster Management Agency said.
Chief Cabinet Secretary Yoshihide Suga said around 48,000 police, firefighters and members of Japanâ€™s Self-Defense Forces were responding to appeals for help.
The weather also disrupted industry. Some automakers halted production as the rain and flooding disrupted supply chains and risked workersâ€™ safety, Kyodo news agency reported.
Mitsubishi Motors Corp halted operations at one plant because it could not get parts, Kyodo said. Mazda Motor Corp stopped production lines at two plants so employees would not have to travel in hazardous conditions.
Reuters could not reach the firms for comment outside business hours. (NAN)