Another alert was also issued for 130,000 people in the city of Toyohashi, also in Aichi, according to the public broadcaster NHK.
In the Wakayama region in the west, several rivers burst their banks.
“We urge residents [en las áreas afectadas] to be extremely vigilant about landslides, floods and rivers that are swollen or overflowing,” government spokesman Hirokazu Matsuno told reporters.
“Extremely heavy rain with thunderstorms is expected over a wide area from western to eastern Japan over the next three days” due to the storm, which started out as a typhoon but eased in intensity.
Shinkansen high-speed trains have been suspended between Tokyo and Nagoya, according to Japan Railwayand NHK said more than 200 flights were cancelled.
Scientists credit climate change with intensifying the risk of heavy rain in Japan and elsewhere, because a warmer atmosphere holds more water.
Heavy rains in 2021 triggered a devastating landslide in the central Japan resort town of Atami, killing 27 people.
Earlier this week, Mawar, then a typhoon, passed just north of the Pacific island of Guam, uprooting trees and leaving tens of thousands of homes temporarily without power.