Humid tropical air
The Meteorological Agency says the downpour was set off by an influx of extremely humid air.
Seawater temperatures near Japan have been high. Rain clouds are more likely to develop in these conditions.
At the same time, typhoon Prapiroon moved northeast over the Sea of Japan. It left behind extremely damp air and a huge band of dense clouds.
These clouds fed humid air into the active seasonal front in the affected areas, which has led to the record-breaking rainfall.
Yasushi Kajihara from Japan Meteorological Agency described what happened:
"Usually, the potential of heavy rain decreases after a storm moves away, but this time was different. The potential remained high. There's been a huge and unprecedented amount of vapor in the air over the past several days, along the Pacific coast of western Japan. I believe an influx of extremely humid air is the main factor behind the persistent record-breaking downpours."
Serious damage across the country
As of the afternoon of July 9th, more than 100 people are dead and dozens still missing in central and western parts of the country.
In Ohzu City, Ehime prefecture, a 100-meter bridge over the Hijikawa River was completely washed away. Flooding of the river has caused serious damage, leaving at least four people dead.
On the remote island of Nuwajima, off Matsuyama City, Ehime prefecture, three people have died. The victims are two elementary school girls and what appears to be their mother. A mudslide hit their house.
The girls' school principal said he was shocked by the sudden disaster. There are just six pupils registered at the school, including the sisters.
A house was washed away at night on July 7th in Fukuyama City, Hiroshima prefecture, when a reservoir collapsed, leaving a three-year-old girl missing. Firefighters and residents began searching for the girl the next morning. But in the afternoon on the same day, the girl was found near her house and was confirmed dead.
Japan's Meteorological Agency says the emergency warnings for extremely heavy rain have all been lifted. But it warns heavy rains have flooded rivers and caused landslides in many areas.
And now, with the mercury rising sharply in the west, people are facing a new threat from heatstroke.