Rain pounded the region from Saturday, with more than 540 millimetres recorded in the city.
The flooding disaster follows a magnitude-7.5 quake on New Year's Day.
For climate change news and analysis, go to News24 Climate Future.
Rescuers combed the debris-strewn banks of a river in central Japan on Monday, searching for drowning victims after homes were swept away in flooding and landslides that claimed at least seven lives.
The river on the Noto Peninsula - an area still reeling from a devastating earthquake in January - overflowed at the weekend, becoming a muddy torrent that inundated roads and a remote hamlet.
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