TV footage showed a muddy mass of broken trees swept into a mountainous residential area by the downpours, which broke records in some areas.
Two people have been reported missing, top government spokesman Hirokazu Matsuno told reporters.
Authorities have warned of an increased risk of landslides and floods.
Public broadcaster NHK said non-compulsory evacuation advisories were issued to 200,000 residents in five regions: Niigata, Yamagata, Fukushima, Ishikawa and Fukui.
Other TV footage showed homes flooded by an overflowing river and another muddy waterway reaching the height of a bridge.
Some shinkansen bullet trains were suspended in the affected areas.
Scientists say climate change is intensifying the risk of heavy rain in Japan and elsewhere, because a warmer atmosphere holds more water.
Strong rain in 2021 triggered a devastating landslide in the central resort town of Atami that killed 27 people.
Previously in the year 2018, floods and also landslides killed more than 200 people in western Japan. This devastating incident happened actually during the country’s annual rainy season. That is such a sad tragedy to witness.