The Mogami River in Yamagata prefecture flooded four areas following an overnight downpour, leaving several towns inundated, chief government spokesman Yoshihide Suga said. Another river overflowed its banks in nearby Akita prefecture, he said.
Suga told reporters no deaths have been confirmed. But he warned people should evacuate from risky areas. A mudslide has isolated an area with more than 500 people, he added.
TV footage showed rescuers paddling rubber boats in residential areas, looking for stranded people, and groups of homes in a sprawling lake of muddy water.
The Yamagata Shinkansen bullet train temporarily stopped running, and some highways were blocked off.
Heavy rainfall was expected throughout Wednesday, including in some areas near Tokyo. The southwestern area of Kyushu was hit with heavy rain earlier this week.