Heavy rain and powerful winds cut power lines and cause flight cancellations.
An 11-year-old boy died after he was swept along by a fast-moving river while trying to pick up a ball, a police official in southern Kagoshima prefecture said.
Public broadcaster NHK earlier said 56 people had been injured.
Television footage showed heavy rain pounding on empty streets and workers mopping floors of train stations.
NHK said several houses and a post office collapsed under a landslide in Kagoshima, while strong winds and landslides damaged dozens of homes in other areas.
Local officials advised over 15,000 households to evacuate as they warned of more flooding and landslides. Around 12,000 people fled to evacuation centres on their own.
“We’re worried. We don’t want to stay home,” one elderly evacuee told NHK television.