The assessment of casualties has been hard because of the widespread area affected by the rainfall, flooding and landslides.
Authorities have warned that landslides could strike even if the rainfall diminishes.
Public broadcaster NHK said another four people were seriously injured and 47 are still missing.
'Around 1,000 people were seeking rescue by Sunday morning, but we don't yet have a complete picture of the disaster, which is enormous, ' Mutsunari Imawaka, a spokesman for the prefecture's disaster management office, said.
A broken embankment is seen in front in flooded Kurashiki city, Okayama prefecture, southwestern Japan.
A government official told AFP a special crisis cell had been created to respond to the disaster and would hold a meeting chaired by Prime Minister Shinzo Abe on Sunday morning.
Television footage showed bridges and cars washed away by raging rivers and floodwaters, with people perched on the roofs of their homes, surrounded by water and awaiting rescue.
Authorities in Japan continued desperate searches on Sunday for victims of flooding and landslides spawned by record rainfall as storms continue to hammer the southern part of the country.
"We've never experienced this kind of rain before", an official at the Japanese Meteorological Agency told reporters.
Some areas have been hit by more than a metre of rainfall, according to the government, while around 48,000 troops, police and firefighters have been deployed for rescue operations, Chief Cabinet Secretary Yoshihide Suga said.More news: China tariffs: What's behind them, who stands to be hurt? | AP business
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At least 4 million people have been advised to evacuate surrounding areas.
Japan Ground Self-Defense Force members use a boat to evacuate a resident from a flooded area caused by heavy rains in Kurashiki, Okayama prefecture, southwestern Japan.
Roads were blocked in some areas and warnings issued on landslides.
"We had fled to the second floor but then the water rose more, so we went up to the third floor", she said.
Residential buildings are damaged by a landslide caused by heavy rains in Sakacho, Hiroshima prefecture, south western Japan.
Two sisters from an elementary school with just six students on the small island of Nuwa in Ehime prefecture also died, according to Reuters.
At least 80 people have died in torrential rains that pummeled wide areas of western Japan.
A woman in her 70s or 80s was reportedly found dead inside a drainage facility in central Japan, local police reported, with a number of people remaining unaccounted for, including a man in Kochi Prefecture whose milk deliver auto may have been washed away by a river.
It is the deadliest rain event in Japan since 2014, when at least 74 people died due to landslides that were triggered by torrential downpours in the Hiroshima region.