Rains falling in Kyushu and Chugoku since the weekend caused flooding along a number of rivers as well as mudslides, closing roads, disrupting trains and cutting the water supply in some areas.
The Japan Meteorological Agency issued an emergency heavy rain warning for Fukuoka and Oita prefectures on the southern main island of Kyushu, urging residents in riverside and hillside areas to take maximum caution.
"The rain is becoming so heavy unlike anything seen before," the agency's forecast director Satoshi Sugimoto told a press conference.
More than 1.7 million residents in vulnerable areas were urged to take shelter.
Chief cabinet secretary Hirokazu Matsuno told reporters the government has set up a task force and is doing its utmost for the search and rescue operation "as we put the people's lives first".
Two people have died and at least six others were missing, according to the Fire and Disaster Management Agency and prefectural officials.
A man was found dead in a vehicle that fell into a swollen river in Yamaguchi prefecture.
In the town of Soeda in Fukuoka prefecture, two people were buried underneath a mudslide.
One was rescued alive, but a woman in her 70s was killed.Â
In the city of Karatsu in Saga prefecture, rescue workers were searching for three people whose houses were hit by a mudslide, the agency said.
Footage on NHK television showed one of the destroyed houses reduced to just a roof sitting on the muddy ground amid floodwater flowing down.
At least three others were missing elsewhere in the region.
Some parts of Fukuoka had received more than 500mm of rain since Friday, more than usually falls in the whole of July, media reported, and another 200mm is expected up to early Tuesday, Sugimoto said.
With Reuters
12°C