Remnants of Typhoon Prapiroon fed into a seasonal rainy weather front fuelled by warm air from the Pacific Ocean - a pattern similar to one that caused flooding in southwestern Japan exactly a year ago that killed dozens on people.
The recent rainfall was unprecedented and disaster experts said torrential rains are becoming more frequent, possibly due to global warming.
"The government is just starting to realise that it needs to take steps to mitigate the impact of global warming," said Takashi Okuma, an emeritus professor at Niigata University who studies disasters.
Municipalities in Japan have been required since 2001 to create and publicise "hazard maps" showing the risk of flooding and landslides. By 2013, 95 percent of municipalities had produced flood hazard maps and 81 percent for landslides, according to the land ministry.
However, experts say many homes in Japan were built in risky areas before the 2001 requirement to distribute hazard maps.
Kurashiki city in Okayama prefecture, where the Mabi district was especially hard hit by this week's floods, distributed a hazard map in 2016, the Yomiuri newspaper said.
Despite orders and advisories to evacuate, which may have been issued too late, some residents appear to have ignored the warnings because they did not know where to go or how to get to safety.
Asked if he knew he lived in a designated risk area, Kenji Ishii, a 57-year-old resident of Mabi district, said: "I'm afraid I did not know that very well".--REUTERS