Since last Monday, more than 20 inches of rain had fallen in Niigata prefecture (state) - nearly one-fifth the annual average.
A 42-year-old woman, who had been missing since Tuesday, was found drowned in a ditch, police said.
Local authorities maintained an evacuation order for more than 12,000 households in the prefecture, where still more rain is expected.
A separate storm farther south, meanwhile, caused floods that killed two men in their 60s and unleashed a landslide that killed a third, in his 70s, according to police.
A 72-year-old woman and a 60-year-old man also were reported missing in the area, where rainfall was heavy Saturday night and Sunday morning.
Authorities advised about 40,000 households along the Asuwa River to seek refuge in shelters. Train services were halted and bridges spanning the river were washed away.
The Self-Defense Forces dispatched troops to help with rescue and cleanup and to offer water services.
The Meteorological Agency warned of more flooding, landslides and overflowing rivers. Accompanied by lightening and gusts of wind, rainfall in Fukui for the 24 hours to midnight could total 14 inches, the agency said.
Television footage from Fukui showed residents wading through streets that had turned into rivers.
The floods are part of the rainy season in Asia and South Asia.
In South Asia - Bangladesh, Nepal, Pakistan and India - 374 people have died as a result of floods in the past few weeks.
In India, at least 5.5 million have been forced to flee their homes.