The national weather agency issued a flood and landslide warning Wednesday for the Sea of Japan coast, with heavy rain expected from eastern to western Japan into Thursday.
The Japan Meteorological Agency issued storm warnings for parts of Shimane and neighboring Tottori prefectures. In Matsue, the prefectural capital of Shimane, the Iu River reached the flood risk level.
The two prefectures ordered about 360,000 and 120,000 residents to evacuate, respectively.
There were reports of damage caused by landslides and flooding at multiple locations in Matsue and Izumo, also in Shimane Prefecture, according to the municipal governments.
The agency said 75 millimeters of rainfall was recorded in Izumo in one hour on Wednesday.
The city government of Matsue put off coronavirus vaccinations for around 200 elderly people scheduled for the day due to the rain.
In central Japan's Shizuoka Prefecture, on the Pacific coast, record rains have loosened the earth in some locations and increased the risk of disasters similar to a large mudslide that occurred there late last week, it said.
The death toll from the mudslide in the Shizuoka city of Atami rose to seven on Tuesday, with 25 people still unaccounted for.