More than 70,000 rescuers are looking for dozens of missing people, and thousands remain in shelters.
In west Japan, residents are picking up the pieces of what remains of their homes after record-breaking torrential rain battered the region, claiming at least 157 lives and leaving 57 people missing.
More than 60 people are still unaccounted for, including those in one of the hardest-hit areas, Hiroshima prefecture, Suga said.
Prime Minister Shinzo Abe at a disaster response meeting Thursday recalled seeing "horrendous" damage during his visit the previous day to Kurashiki city, where a river broke through its embankment and flooded a wide area.
Meanwhile, the Ministry of Land, Infrastructure, Transport and Tourism is continuing efforts to drain the area. Since Thursday, landslides and flooded rivers have trapped many people in their houses or on rooftops.
A damaged vehicle is seen in floodwater on July 10, 2018 in Kurashiki, Japan.
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"The area became an ocean", 82-year-old resident Nobue Kakumoto told AFP Sunday, surveying the scene.
"Why didn't I tell her to evacuate?" he said, regretting that he told his wife not to worry about the intensifying rain when he last contacted her via online messaging app Line on Friday night.
Rain tapered off across the western region on Monday to reveal blue skies and a scorching sun that pushed temperatures well above 30 Celsius (86 Fahrenheit), fuelling fears of heat-stroke in areas cut off from power or water especially as people worked to clear their homes and work places of rubble and mud.
"We are not able to use the toilet or take baths and our food stockpile is running low", said one of the flood affected resident. "I had wanted my daughter to wear it", Fukuda said, her eyes filling with tears.
The United Nations said Secretary General Antonio Guterres had written to Prime Minister Shinzo Abe offering support.
Abe visited an evacuation center Wednesday in a hard-hit flood zone in western Japan.
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Some cities within Okayama prefecture saw flooding of almost 30 percent of the total area, while the number of partially or fully destroyed homes nationwide exceeds 10,000.
A man walks past a damaged street in Saka, Hiroshima prefecture.
The figures are expected to substantially increase as municipal authorities have yet to finish assessing the scale of the damage.
In the town of Saka, Eiichi Tsuiki opted to stay in his home, and survived only by moving to the top floor as flood waters rose, washing cars away outside.
But Farm Minister Ken Saito said that damage caused to agriculture, including mountain forests, paddy fields and reservoirs, had already topped 7 billion yen (63 million US dollars).
The downpours continued to hit businesses although some companies have begun resuming operations.
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Automakers including Mazda Motor Corp (7261.T) and Daihatsu Motor Co suspended operations at several plants on Saturday due to a shortage of parts or unsafe conditions.