Heavy rainfall has hammered southern Japan for the third day, prompting new disaster warnings as the government put the death toll at 48 with 28 others presumed dead.
Japanese government spokesman Yoshihide Suga said the whereabouts of 92 people are unknown, mostly in the southern area of Hiroshima prefecture.
More than 100 reports of casualties had been received, such as cars being swept away, he said.
“Rescue efforts are a battle with time,” Prime Minister Shinzo Abe told reporters. “The rescue teams are doing their utmost.”
The assessment of casualties has been difficult because of the widespread area affected by the rainfall, flooding and landslides.
Authorities warned landslides could strike even after rain subsides as the calamity shaped up to be potentially the worst in decades.
Kochi prefecture, on Shikoku, issued landslide warnings almost over the entire island.
Public broadcaster NHK TV showed overturned cars on roads covered with mud. A convenience store worker, who had fled to a nearby rooftop, said water had reached as high as his head.
The Japanese government set up an emergency office, designed for crises such as major earthquakes.
Some people fled to rooftops and balconies and waved furiously at hovering rescue helicopters. Military paddle boats were also being used to take people to dry land.
Okayama prefecture said three people had died, six others were missing and seven were injured, one of them seriously.
Six homes were destroyed, while nearly 500 were flooded. Evacuation orders or advisories were issued to more than 910,000 people, the prefecture said in a statement.
Kyodo news service reported several deaths in a landslide in Hiroshima and more bodies were retrieved from collapsed housing in the ancient capital of Kyoto, both areas where the rainfall was heavy in the past few days.
Throughout the hard hit areas, rivers swelled and parked cars sat in pools of water.
Japan has sent troops, firefighters, police and other disaster relief. People have also taken to social media to plead for help.
In Ehime prefecture, a woman was found dead on the second floor of a home buried by a landslide, Kyodo said.
Also in Ehime, two schoolgirls and their mother who got sucked into a mudslide were pulled out but could not be revived, it said.