Shinzo Abe, Japan's Prime Minister, has warned of a "race against time" to rescue flood victims as authorities issued new alerts over record rains that have killed at least 48 people and left dozens missing.
The torrential downpours have caused flash flooding and landslides across central and western parts of the country, prompting evacuation orders for more than two million people.
"Rescues, saving lives and evacuations are a race against time," Mr Abe said as he met with a government crisis cell set up to respond to the disaster.
"There are still many people whose safety has yet to be confirmed," he added.
Top government spokesman Yoshihide Suga said the death toll in days of record rains now stood at 48, but the toll was expected to rise further. National broadcaster NHK said at least 62 people were dead and 44 missing.
The Japan Meteorological Agency said three hours of rainfall in one area in Kochi prefecture reached an accumulated 26.3 centimeters (10.4 inches), the highest since such records started in 1976.
"We've never experienced this kind of rain before," an official at the Japanese Meteorological Agency told a news conference. "This is a situation of extreme danger."
The unprecedented downpours have wreaked havoc primarily in the west of the country.
The rain has completely blanketed some villages, forcing desperate residents to take shelter on their rooftops with flood water swirling below as they wait for rescue.
In western Okayama prefecture, around 200 people including children and elderly people were trapped in a hospital after a river burst its banks and flooded the surrounding area.
"The electricity and water has been cut off. We are suffering water and food shortages," a nurse told public broadcaster NHK.
Over 50,000 rescue workers, police and military personnel have been mobilised to respond to the disaster, which has left entire villages submerged by flooding, with just the top of traffic lights visible above the rising waters.
"My house was simply washed away and completely destroyed," Toshihide Takigawa, a 35-year-old employee at a gas station in Hiroshima, told the Nikkei daily on Saturday.
"I was in a car and massive floods of water gushed towards me from the front and back and then engulfed the road. I was just able to escape, but I was terrified," 62-year-old Yuzo Hori told the Mainichi Shimbun daily in Hiroshima.
Though the typhoon began last week, the worst of the rain hit from Thursday, when a construction worker was swept away by floodwaters in western Japan.
The toll has risen steadily since then, and the conditions have made rescue operations difficult, with some desperate citizens taking to Twitter to call for help.
"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.
"The kids could not climb up to the rooftop," she said. "My body temperature has lowered. Rescue us quickly. Help us."
In some place rescuers were using boats, or helicopters to airlift those affected to safety.
Several major manufacturers, including carmakers Daihatsu and Mitsubishi, said they had suspended operations at plants in the affected areas.
The disaster is the deadliest rain-related crisis in Japan since 2014, when at least 74 people were killed in landslides caused by torrential downpours in the Hiroshima region.