Another 61 were missing, national broadcaster NHK said, and more rain was set to hit some areas for at least another day
Unprecedented rains that have killed at least 69 people also stranded 1,850 in the western Japanese city of Kurashiki on Sunday, including about 130 at a hospital, with rescuers using helicopters and boats after rivers surged over their banks.
Kurashiki, with a population of just under 500,000, has been hit hardest by the torrential rains that pounded some parts of western Japan with three times the usual precipitation for a normal July.
Television footage showed people, apparently patients and staff, waiting to be rescued on a balcony at Mabi Memorial Hospital, while many cars floated in muddy water and a person was rescued by helicopter from an elderly care facility.
The overall death toll from the rains in Japan rose to at least 69 on Sunday from 49 overnight after floodwaters forced several million people from their homes, media reports and the Fire and Disaster Management Agency said.
The death toll is the highest caused by water disasters since 2014 when 77 people were killed in heavy rain which set off landslides in Hiroshima in western Japan.
Another 61 were missing, national broadcaster NHK said, and more rain was set to hit some areas for at least another day.
The rain set off landslides and flooded rivers, trapping many people in their houses or on rooftops.
“We’ve never experienced this kind of rain before,” an official at the Japanese Meteorological Agency (JMA) told a news conference. “This is a situation of extreme danger.”
Among the missing was a 9-year-old boy believed trapped in his house by a landslide that killed at least three others, including a man in his 80s.
“All I have is what I’m wearing,” a rescued woman clutching a toy poodle told NHK. “We had fled to the second floor but then the water rose more, so we went up to the third floor.”
Japan’s government set up an emergency management centre at the prime minister’s office and some 54,000 rescuers from the military, police and fire departments were dispatched across a wide swath of southwestern and western Japan.
“There are still many people missing and others in need of help, we are working against time,” Prime Minister Shinzo Abe said.
Emergency warnings for severe rain remained in effect for three prefectures, with 300mm (11 inches) predicted to fall by Monday morning in parts of the smallest main island of Shikoku.
Evacuation orders remained in place for some 2 million people and another 2.3 million were advised to evacuate, although rain had stopped and floodwaters receded in some areas. Landslide warnings were issued in more than a quarter of Japan’s prefectures.
“My husband couldn’t make it home from work since the road was flooded, and since it was pouring down rain I didn’t have enough courage to walk to an evacuation center with two infants after dark,” one woman wrote on Twitter, without giving further details.
The rain began late last week as the remnants of a typhoon fed into a seasonal rainy front, with humid, warm air from the Pacific making it still more active - a pattern similar to one that set off flooding in southwestern Japan exactly a year ago that killed dozens. The front then remained in one place for an unusually long time, the JMA said.
Roads were closed and train services suspended in parts of western Japan. Shinkansen bullet train services resumed on a limited schedule after they were suspended on Friday.
Automakers including Mazda Motor Corp and Daihatsu Motor Co suspended operations at several plants on Saturday due to a shortage of parts or dangerous conditions. They were set to decide later on Sunday on plans for the coming week.
Electronics maker Panasonic Corp said one plant in Okayama, western Japan, could not be reached due to road closures, although it had been closed for the weekend anyway. A decision about next week would be made on Monday, it said.
While the Japanese government monitors weather conditions closely and issues warnings from an early stage, the fact that much of the country outside major cities is mountainous and building takes place on virtually every bit of usable land leaves it vulnerable to disasters.