Emergency teams are searching for another 15 people who are missing.
Rivers burst their banks, destroying buildings and roads after more than 50cm (20in) of rain fell on parts of Kyushu, Japan's southernmost island, over a 12-hour period on Wednesday.
Rescuers are working through thick mud to try to reach stranded survivors. Hundreds have already been evacuated.
The worst-hit areas are in Fukuoka prefecture.
Announcing the revised death toll, Chief Cabinet Secretary Yoshihide Suga said the region was expected to see further heavy rain on Saturday.
About 12,000 police, military, firefighters and coast guard personnel have taking part in the rescue operation.
resources : bbc
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