More than 1.6 million people were ordered to evacuate their homes, while 3.1 million were put on high alert and urged to do so. Nevertheless, Kyodo said, many had remained at home.
Chief Cabinet Secretary Yoshihide Suga said 54,000 police officers, firefighters, and members of Japan's Self-Defence Forces and coast guard had been mobilised in the rescue effort, Kyodo reported, with TV footage showing them using boats and helicopters to bring people to safety.
Public broadcaster NHK said flooding and landslides were hindering rescue efforts and repeatedly urged people not to lose hope.
Among the dead was a 3-year-old girl whose home was hit by a landslide in Hiroshima prefecture, Reuters reported.
"It's very painful," said one elderly man watching nearby. "I have a granddaughter the same age. If it were her, I wouldn't be able to stop crying."
Two sisters from an elementary school with just six students on the small island of Nuwa in Ehime prefecture also died, according to Reuters. The younger, a first-grader, was a star and the hope of the depopulated island, the principal told NHK.
The western Hiroshima prefecture was hit the hardest by landslides, which claimed 37 lives, while 21 people died in Ehime, NHK reported.
In August 2014, 77 people died in Hiroshima when torrential rain triggered massive landslides, but one resident told Kyodo that the rains were heavier this time.
Auto manufacturers Mitsubishi and Mazda were forced to halt production at some factories because they could not get parts or did not want to force employees to travel to work in dangerous conditions, Kyodo reported.
