More than 30 000 households in Fukui prefecture were advised to evacuate after it was hit by torrential rains accompanied by thunderstorms and strong winds.
A total of 284mm of rain had fallen in parts of Fukui from Saturday evening to Sunday morning, with another 120mm predicted by midnight, the Meteorological Agency said.
The total rainfall in the 24 hours up to midnight was likely to reach 350mm in some areas, it added, warning of a growing danger of floods and landslides.
Television footage showed muddy, swollen rivers threatening to burst their banks and bridges choked with brush and trees.
In one scene on NHK national television, muddy water trickled from cracks in a concrete breakwater.
"The water rose above the floor of our house in less than three hours this morning," one man told NHK as he sat in a temporary shelter. "It's quite scary."
Some train services in the affected area were halted.
Torrential rains in the northern prefecture of Niigata on Tuesday caused swollen rivers to burst their banks, touched off landslides, forced thousands to evacuate and left thousands more trapped in their homes awaiting rescue.
The death toll in that flooding rose to 15 on Sunday after one more body was found. Virtually all the victims were elderly people in their 70s and 80s.
The rain is forecast to continue over the next hours to come. If you see the names a little different is that they are in Spanish and the temperatures are in Celcius (ºC).