Since then, 13 more people have died from cardiac arrest, bringing the total number of deaths to 100, according to Chief Cabinet Secretary Yoshihide Suga.
With emergency warnings about rain raised, the country is now focusing its attention on search and rescue efforts. The police, the fire departments and the army are exploring the affected areas for the dozens of missing or disappeared people.
"We will unite and move quickly to deliver those needs to the victims of the disaster by coordinating closely with the local government," Prime Minister Shinzo Abe met with the disaster response working group and also noted "the need for future "to improve evacuation centers and temporary housing.
While the authorities search for the disappeared, residents begin cleaning up, wade through flooded houses and streets.
Thousands of houses have been damaged, and even those that remain intact have been impacted. Almost 17,000 homes still do not have electricity and telephone lines are crossed by several prefectures.
The fact that many railroads and roads are closed, too flooded to operate and that many affected areas are out of reach, is an additional problem for repairs. 
The rains started at the end of last week and intensified during the weekend. Rivers overflowed, landslides crushed buildings and cars were washed away by floodwaters.
"Record rainfall in several parts of the country has caused rivers to explode and trigger large-scale floods and landslides in several areas," said Cabinet Secretary Suga said on Sunday.
Two million people were forced to flee their homes, advised or ordered by the government to evacuate. Some, unable to leave, took refuge on the rooftops when the floods swallowed entire streets.
In Kurashiki, near Okayama, soldiers were deployed to take the elderly residents of their homes to the boats.
Kazuhiko Ono, owner of a second-hand bookstore in the city of Hiroshima, was not able to return home and shop when the rains came. His wife and children took refuge on the second floor of his house, while the store was filled with water.
"I'm so sad to have lost a lot of books," Ono said. "I can not find them anymore."
The prefectures of Hiroshima and Ehime were some of the most affected, although another nine also suffered a great impact.
Images of Kuyashiki, a city on the south coast of Okayama prefecture, show cars overturned or buried in mud.
Suga warned that although rain warnings had been raised, residents should beware of landslides. Those who participate in cleanup efforts should be careful with heat stroke, since the next few days are expected to be warm and clear
About 73,000 people have been mobilized for search and rescue efforts.