It is the highest death toll caused by rainfall that Japan has seen in more than three decades.
Rescuers are now digging through mud and rubble in a race to find survivors, as dozens are still missing.
About two million people have been evacuated from the region after rivers burst their banks.
Authorities have opened up school halls and gymnasiums to those who have been displaced by the rainfall.
There remains a risk of landslides, with rain-sodden hilltops liable to collapse.
"I have asked my family to prepare for the worst," 38-year-old Kosuke Kiyohara, who has not heard from his sister and her two sons, told AFP.
Prime Minister Shinzo Abe has cancelled an overseas trip to deal with the flood crisis.
More than 70,000 rescue workers, including the fire service and the army, are involved in the relief effort.