The prime minister’s office said a task force had been established to coordinate a response to the rains.
“We have received reports that several rivers have flooded… and that landslides have occurred in various parts” of the country, top government spokesman Hirokazu Matsuno told reporters.
“The government is doing its best to get a complete picture of the damage and taking measures under a policy of ‘people’s lives first,’” he added.
He warned torrential rain was forecast across much of the country on Tuesday.
“If you feel your life is in danger, even just a little, don’t hesitate to act,” he said.
In Fukuoka’s Asakura City, officials said the rain was believed to have peaked but there were still fears about flooding.
“Water levels in rivers are rising so we’re vigilant against the possibility of overflowing,” local official Takaaki Harano told AFP.
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 over a week in the region.
“The area is very wet due to intermittent rainfall for over a week,” Yoshiyuki Toyoguchi, land ministry official in charge of rivers, told reporters.
“Even with a little rain, river levels tend to rise quickly, which will increase the risk of flooding.”
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.