The prefectures of Kumamoto and Kagoshima have been worst hit, with hundreds of thousands of people advised to evacuate, reports the BBC.
More than 40,000 rescue workers in the south-west were still searching for survivors on Monday, after record rains caused landslides and rivers to burst their banks on Saturday.
Another 30 cm of rain is expected in the next two days.
According to the the BBC report, while it is normal for Western Japan to bear the brunt of the rains sweeping out from the tropics during monsoon season, the last two days have seen truly extraordinary amounts of rain falling over the island of Kyushu.
Japan's Meteorological Agency said such rainfall had never been seen before in the region.
On Saturday night, the Kuma river burst through its levees in numerous places inundating low-lying settlements.
Fourteen victims were found in one nursing home, after river waters flooded the ground floor. Another 50 were rescued.
It is Japan's worst disaster since Typhoon Hagibis struck last October, killing some 90 people.
Meanwhile, evacuation centres are running at lower capacity because of the risk of coronavirus, with fire department official Toshihiko Nakamura telling the Kyodo News agency that they had sent some evacuees to another centre due to social distancing rules.
Others have opted to shelter in their cars for fear of infection.