With 30% of their inventory damaged, owners of Preloved Books now face the daunting task of rebuilding from scratch
"Without water, we can't really clean anything up. We can't wash anything," one man told NHK television.
The government has sent water trucks to the disaster area, but supplies remain limited.
More than 70,000 military, police and firefighters toiled through the debris in a grim search for the missing.
Some teams shovelled dirt into sacks and piled the bags into trucks. Others used diggers and chainsaws to work through landslides and splintered buildings.
Many areas were buried deep in mud that smelled like sewage and had hardened in the heat, making the search more difficult.
Disasters set off by torrential rains have become more frequent in Japan, perhaps due to global warming, experts say. Dozens of people died after similar rains caused flooding around the same time last year.
"It's an undeniable fact that this sort of disaster due to torrential, unprecedented rain is becoming more frequent in recent years," Chief Cabinet Secretary Yoshihide Suga said at a news conference in Tokyo.
"Preserving the lives and peaceful existence of our citizens is the government's biggest duty. We recognize that there's a need to look into steps we can take to reduce the damage from disasters like this even a little bit," he added.
With 30% of their inventory damaged, owners of Preloved Books now face the daunting task of rebuilding from scratch
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There are also increasing accounts, on social media and online forums, of tourists and residents across the city having to pay inflated prices for taxis