A truck and two cars are seen abandoned outside a convenience store in Kurashiki, Okayama Prefecture, on Sunday.
The Japan Meteorological Agency said three hours of rainfall in one area in Kochi prefecture reached an accumulated 26.3 cm, the highest since such records started in 1976.
"The situation is extremely unsafe", wrote a Twitter user in Kochi, a city on the smallest main island of Shikoku, where the rain has been especially intense.
Local authorities said a total of 20 people were killed in rain-related accidents, while public broadcaster NHK said the death toll had risen to 38 with 50 others unaccounted for.
A woman who had gone missing after leaving her home in Kameoka, Kyoto Prefecture, in her auto was found dead in a river in Nose, Osaka Prefecture, on Friday.
"All I have is what I'm wearing", a rescued woman clutching a toy poodle told NHK television.
"The kids could not climb up to the rooftop", she said.
On the morning of July 8, the government set up an emergency headquarters in response to the heavy rainfall in western Japan and held its first meeting at the prime minister's office.
Two Contenders Remain as Trump Mulls Supreme Court Pick
He served with the president's sister on the Third Circuit, and she apparently recommended Hardiman for the Supreme Court. Kavanaugh played a key role in drafting the Starr report, which urged the impeachment of President Bill Clinton.
"The situation is extremely serious", Shinzo Abe, the prime minister, said as he called for an "all-out" rescue effort.
In Motoyama, a town on Shikoku island, about 600 km (373 miles) from the capital Tokyo, 583 mm (23 inches) of rain fell between Friday and Saturday morning, the agency said.
The special warnings indicate people in the affected regions should remain on high alert, but are not compulsory evacuation orders.
As many as 1.3 million were forced to evacuate as the flooding worsened. The front then remained in one place for an unusually long time, the JMA said.
Transportation services have been severely disrupted since Thursday, the transport ministry said, with a number of Shinkansen bullet train services partially disrupted and major arterial highways partially closed.
Mitsubishi Motors Corp. halted operations at its Okayama plant as it was unable to procure parts, while Daihatsu Motor Co., a mini-vehicle making unit of Toyota Motor Corp., said it had suspended production at two plants in Osaka and Kyoto for the same reason, Kyoto reported. A decision about next week would be made on Monday.
Landslide warnings have been issued in over a quarter of the nation's prefectures.