A heavy band of precipitation dumped record-breaking amounts of rain in some parts of the Kyushu area through Monday, causing rivers to overflow and sodden earth to collapse in landslides.
At least three people are confirmed to have died in the rains, government spokesman Hirokazu Matsuno told reporters on Tuesday, adding officials were investigating whether another three deaths were linked to the disaster.
Three people remain missing and two have been reported lightly injured, he added.
"We express our condolences to those who died, and our heartfelt sympathy towards those who were affected by the disaster," Matsuno said.
Some remote communities remain effectively cut off by flooding and other damage, but the safety of residents there has been confirmed.
Transport remained disrupted as of early Tuesday, with some train services stopped and highways blocked, and 1,400 homes were without power.
In Saga region's Karatsu, members of Japan's military were digging through the soil and debris left by a deadly landslide that engulfed homes.
The downpours, which forecasters had warned risked being the region's "heaviest rain experienced", prompted evacuation notices for hundreds of thousands of people.
Japan is currently in its annual rainy season, which often brings heavy downpours, and sometimes results in flooding and landslides as well as casualties.
Scientists say climate change is intensifying the risk of heavy rain in Japan and elsewhere, because a warmer atmosphere holds more water.
The weather agency said it had already been raining for more than a week in the region before the heavy downpours that arrived Sunday night.
And while the sun was shining in many areas on Tuesday, officials have warned of more rain in the forecast, which could loosen already sodden ground.
Landslides are a particular risk in Japan during heavy rains because homes are often built on plains at the bottom of hillsides in the mountainous country.
In 2021, rain 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 rainy season.
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