Rescuers are now digging through mud and rubble in a race to find survivors, as dozens are still missing.
About two million people have evacuated the region after rivers burst their banks.
"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 also cancelled an overseas trip to deal with the flood crisis.
Flood warnings are still in effect for some of the worst hit areas, including Okayama prefecture.
But more settled weather is expected over the next few days which is likely to help with rescue efforts.
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