The toll has risen steadily since then, and the conditions have made rescue operations hard, with some desperate citizens taking to Twitter to call for help.
Record downpours prompted authorities to order about 1,932,000 people to evacuate their homes mainly in western Japan, according to the Fire and Disaster Management Agency, but NHK said the figure had risen to almost 3.2 million.
Rivers surged and the ground loosened, causing some people to be swept away by rushing water and others to be buried alive in landslides.
The Japan Meteorological Agency said three hours of rainfall in one area in Kochi prefecture reached an accumulated 26.3 centimetres, the highest since such records started in 1976.
The torrential downpours have caused flash flooding and landslides, with local media putting the toll around 50 dead with dozens more unaccounted for.
"It's very painful", said one elderly man watching nearby. "I was just able to escape, but I was terrified", 62-year-old Yuzo Hori told the Mainichi Shimbun daily in Hiroshima.
An emergency management centre has been set up at the Prime Minister's office to handle the situation and some 54,000 military, police and fire department personnel have been dispatched to the flooded areas.
At a meeting of an emergency center the government set up Sunday, Prime Minister Shinzo Abe called for all-out efforts for search and rescue.
The rain began late last week as the remnants of a typhoon fed into a seasonal rainy front.
Businesses continued to be affected, with automaker Mazda Motor Corp. and Daihatsu Motor Co., a minivehicle making unit of Toyota Motor Corp., suspending operations in factories in Kyoto, Hiroshima and Yamaguchi.
The agency said that atmospheric conditions from western to northern Japan are set to remain very unstable owing to warm and moist air flowing into a low-pressure system and an active front close to northern Japan. "I have never seen anything like this", he said, standing in shock before the house where he and his wife raised their three daughters, all now adults. Some 250 people had to flee their homes and the prefecture identified one fatality as a 52-year old woman.
Flooding and storms in western and central Japan killed at least two people, local reports said. Dozens more remained missing. "I don't know what is where".
Japan's Self-Defense forces rescue people by boats from Mabi Memorial Hospital, which was isolated after flood damage.
Photo albums and other family possessions were jumbled together with debris on the floor.
The death toll from record rains that have devastated parts of Japan rose on Monday (Jul 9) to 75, according to an official tally, as rescue workers and troops struggled in the mud and water to save lives.