Tens of thousands of rescue and recovery workers and volunteers were searching for people still missing.
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.
Desperate family members of missing locals waited nearby for word of their relatives.
In one part of Kumano, the nose of a white auto was just visible underneath the top floor of a home that had been torn from the rest of the building and swept down a hillside.
"We'll cut through all the bureaucracy to secure the goods people need for their lives, to improve life in the evacuation centres - such as air-conditioners as the hot days continue - and then secure temporary housing and the other things people need to rebuild their lives", Mr Abe said. A series of quakes in Kumamoto in 2016 led to the deaths of more than 200 people, according to the Japanese Red Cross Society.
In western Okayama prefecture, major rescue operations took place on Sunday to evacuate several hundred people including children and the elderly from a hospital.
"We've never experienced this kind of rain before", an official at the Japanese Meteorological Agency (JMA) told a news conference.
"We want to demonstrate what we have been training for as a center for summarizing and resolving problems such as food poisoning at evacuation centers, and secondary harm accompanying prolonged evacuation", said Yoko So, a doctor who leads the team of experts in public health.More news: Eleven people from Alaska plane crash saved
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"It's not raining today but we must stay alert for the possibility of landslides", she told AFP.
Flash floods and landslides across central and western areas have sparked evacuation orders for more two million people.
In the town of Mihara, roads were transformed into muddy flowing rivers, with dirt piled up on either side as flood water gushed around the wheels of stranded cars.
"I can't go back if I wanted to", the 66-year-old retired Self-Defense serviceman said, holding a bird cage in which the birds chirped.
Flooded rice fields in Mihara. His wife and children took shelter in the second floor of their home, while the store filled up with water.
"I've lived here for 40 years".
And with the end of the rains, searing heat brought new risks, as blazing sun and temperatures up to 35 Celsius (95 Fahrenheit) posed challenges for people living in modestly equipped shelters or damaged homes with no electricity or running water.