Parts of Nagano and Gifu, including areas known for scenic mountain trails and hot springs, have been flooded by massive downpours that have lasted for nearly a week.
More than 300 people, including hotel employees and visitors, were trapped in Kamikochi, as floods and mudslides hit a main road connecting the town to Matsumoto, another tourist destination in Nagano. All of the stranded people were safe, prefectural officials said.
In neighboring Gifu, hundreds were also isolated in the hot spring towns of Gero and Ontake.
Searching continued for a dozen people still missing in Kumamoto and several others elsewhere on the island. In Oita prefecture, a family of four running an inn in the famous hot spring town of Yufuin was missing.
Floodwaters also ravaged local produce ready for shipment to consumers. An eel farm in Kagoshima was hit by rains just before Japan's “unagi” season later this month.
“I can't ship them, or even go near the place to feed them or change the water," eel grower Kazuya Kusuda told TBS television.
The floods are a further blow to an economy already hit by the coronavirus, just as Japan was returning to business as usual.
Kumamoto on Thursday started accepting dozens of volunteers to help residents clean their homes, but they could only be from within the prefecture and temperature checks and masks were required due to the coronavirus concerns.
Hundreds of thousands of people were in areas under evacuation advisories, but leaving wasn’t mandatory and the number who sought shelter was not known.
Japan is at high risk of heavy rain in early summer when wet and warm air from the East China Sea flows into a seasonal rain front above the country. In July 2018, more than 200 people, about half of them in Hiroshima, died from heavy rain and flooding in southwestern Japan.
Follow Mari Yamagauchi on Twitter at https://www.twitter.com/mariyamaguchi