Evacuation orders went out in some outlying parts of Kyoto, with the Kyodo news agency saying about 16,000 people were affected. He added that 48,000 rescue workers are engaged in search and rescue operations in disaster-hit areas.
A man in the far western city of Hiroshima died after falling off a bridge into a river, while a 77-year-old man in Takashima city, Shiga prefecture, was killed after being swept into a canal as he worked to remove debris, NHK said.
Record downpours prompted authorities to order some 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.
Authorities announced new evacuation orders on Friday, bringing the number of people told to leave their homes to 210,853, a lot of them in western Japan. Image: AAPWomen and children have died as a result of the floods.
At least 10 people are believed to have been buried alive by mudslides in Hiroshima Prefecture, according to Kyodo News.
In Seiyo in Ehime Prefecture, five people were confirmed dead due to the torrential rain, including people swept away in a vehicle.
Local authorities said a man in his late 50s has been pronounced dead after being found in an inundated river in Hiroshima Prefecture.
Hundreds of people have been injured, and dozens of homes have been completely destroyed in the disastrous downpours.
Rescuers were searching for 46 missing people on Saturday.
Military water trucks were rushing to areas where water systems were no longer working, Okayama prefecture said.
In a wide area of southwestern Japan to western Japan, rivers were swollen and overflowing, and bridges were washed away, while transport was disrupted, with shinkansen bullet train services suspended in most parts of western Japan.
The weather also hit industry. Two other people were also unaccounted for in Fukuoka prefecture, the agency said.
The government set up a liaison unit in the crisis management center of the prime minister's office to gather information.
On Saturday, Abe warned at an emergency government meeting that "the situation is extremely serious" and ordered his government to "make an all-out effort" to rescue those affected. Although the JMA subsequently lifted the warnings in four of the prefectures, the agency cautioned that heavy downpours could again hit later on July 7 or 8 even in areas where rain had previously eased, and urged people across the country to take caution.