Japan's Self Defence Forces dispatched 180 personnel and 50 vehicles to Kyoto as trains across western and central Japan were stopped, including part of one Shinkansen bullet train line.
Agency official Minako Sakurai told reporters heavy rain was forecast to continue until Sunday in western and eastern Japan.
In August 2014, 77 people died in Hiroshima when torrential rain triggered massive landslides that destroyed homes.
"Water came to the middle of the second floor", a woman in Kurashiki, Okayama wrote, posting a picture of her room half swamped by flooding.
Rescue workers dug into the dirt as landslides crushed houses in the same region, while several people evacuated to their rooftops as floods swamped entire residential areas in part of the Okayama region.
More than 4.7 million people were sent evacuation orders and 48,000 military, police and fire brigade officers are continuing to help in search missions around the country. It is the first time that the JMA has issued emergency heavy rain warnings in eight prefectures at the same time since the agency launched the system in 2013.
A woman in her 70s or 80s was reportedly found dead inside a drainage facility in central Japan, local police reported, with a number of people remaining unaccounted for, including a man in Kochi Prefecture whose milk deliver auto may have been washed away by a river.
Hiroshima Prefecture was hit the hardest by landslides that claimed 22 lives, while 18 died in Ehime Prefecture, with others killed in Osaka, Shiga, Hyogo, Okayama, Yamaguchi and Fukuoka prefectures. Several more people were missing, including one whose auto was swept away as he delivered milk in the early morning hours, NHK national television said. One person died when floodwaters sucked him into a drainage pipe, and the other victim, an elderly woman, was killed by strong winds, the report added.
Television footage showed muddy water flowing out of rivers in parts of the region, including the scenic Arashiyama area in western Kyoto where riverbanks and streets were flooded.
The agency warned that Japan's Kinki region, which includes Kyoto, Hyogo and Osaka prefectures, could be particularly hard-hit by downpours, escalating the risk of floods, landslides, lightning and tornadoes.
The government set up a liaison unit in the crisis management center of the prime minister's office to gather information.