Shanshan, which at landfall was one of the fiercest typhoons to hit Japan in decades, pummelled Kyushu island on Thursday, but its speed has eased to 90 kilometres (56 miles) per hour from 252 kph.
The typhoon killed at least six people and injured over 120, according to the Fire and Disaster Management Agency.
Now downgraded to a tropical storm, Shanshan was located off the western Wakayama region on Saturday and moving east.
ANA and Japan Airlines cancelled around 60 domestic flights for Saturday, affecting almost 7,200 passengers.
Shinkansen bullet trains in the central city of Nagoya were also suspended.
"Please remain vigilant for landslides, flooding and overflowing rivers," the Japan Meteorological Agency warned.
A city in central Gifu region issued a top evacuation warning to its 2,000 residents near an overflowing river, while some cities in northern Hokkaido saw heavy rain.
More than 32,000 households in southern Kagoshima region, where Shanshan made landfall on Thursday, still had no power, according to the operator.
Scientists say climate change is intensifying the risk of heavy rain in Japan and elsewhere because a warmer atmosphere holds more water.
Strong rain in 2021 triggered a devastating landslide in the central resort town of Atami that killed 27 people.
And in 2018, floods and landslides killed more than 200 people in western Japan during the country's annual rainy season.
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