State broadcaster NHK said more than 500 millimeters of rain fell in parts of Niigata prefecture in the past 24 hours before 1300 (0400 GMT).
Television footage showed bridges running aground and roads flooded with water. Part of the Shinkansen high-speed train line was also suspended. The Fire and Disaster Management Agency said about 500,000 people have been ordered to evacuate from Niigata, Ishikawa and Yamagata.
There were no reports of deaths. While most of the affected areas are in rural areas, they also include a number of factories. Major chip maker Renesas Electronics temporarily halted operations at its plant in Yamagata, northern Japan, after authorities issued a heavy rain warning Wednesday night but said work was almost back to normal.
In 2021, heavy rains caused a massive landslide in the coastal resort of Atami (central Japan), which killed 27 people. In 2018, floods and landslides killed more than 200 people in western Japan during the annual rainy season.
Scientists say global warming is causing more rain in Japan than anywhere else in the world, and a warmer atmosphere is holding more water.
