The deluge set records by up to three times the average monthly rainfall for July in several areas, with at least 119 weather-point locations reporting record rainfall.
Japan is famously prone to natural disasters including earthquakes and tsunamis, and is generally considered well-prepared to cope. "My husband couldn't make it home from work since the road was flooded, and since it was pouring down rain I didn't have enough courage to walk to an evacuation center with two infants after dark", one woman wrote on Twitter, without giving further details. Wire services reported the death toll to be the highest in a Japanese weather-related disaster since two typhoons struck in August and September 2011, killing almost 100 people.
The archipelago is battered annually by an average of six typhoons, from around July to October or November.
In Kurashiki, the receding floods have left a layer of silt on everything that was underwater. In this area, rainfall rates at times exceeded three inches per hour.
Many lost their lives after their homes were swept away by floods or were crushed by landslides.
"In addition, Japan's earth is geologically diverse, with tectonic plates and volcanic geological layers, - in a nutshell, it's weak", said Hiroyuki Ohno, head of the Sabo (sand erosion control) and Landslide Technical Centre.
People fled to rooftops and balconies in the city of Kurashiki, at the mouth of the Takahashi River, about 670 kilometers (415 miles) from Tokyo. Many people lined up to receive water in temperatures reaching 34 degrees Celsius.
But the project is ongoing, and many remain in harm's way.
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Delivery companies Sagawa Express Co. and Yamato Transport Co. and cargo service Japan Freight Railway Co. said some of their shipments to and from the flooded areas have been suspended or reduced.
The assessment of casualties has been hard because of the widespread area affected by the rainfall, flooding and landslides.
Officials said the overall economic impact was not clear.
"This human nature means people can't react to disasters like landslides and flash floods, which occur suddenly", he told AFP.
He said the government would also send medicines to Japan. He clasped one man's hands as they spoke.
Many residents may simply have been lulled into a false sense of security by years of experience with severe, but not deadly, weather systems.
Later he told reporters the government would do everything it could to help the survivors. "We are carrying out rescue operations around the clock", Yoshihide Fujitani, a disaster management official in the prefecture, told AFP.
Hiroshima and the surrounding villages were saturated with heavy rains and damaging mudslides Sunday, leaving 10,000 evacuated and over 100 dead.