Evacuation orders have been issued for almost 170,000 people in nine prefectures in the Kansai and other regions, including those affected by last month's strong quake in Osaka Prefecture, according to the Fire and Disaster Management Agency.
In Motoyama, a town in Shikoku island, 583 millimeters (23 inches) of rain fell in the 24 hours between Friday and Saturday mornings, the Meteorological Agency said.
These prefectures include those in the Kansai region, including Osaka, which is still reeling from a powerful natural disaster that hit the area in June.
An aerial view shows local residents seen on the roof of submerged house at a flooded area as they wait for a rescue in Kurashiki, southern Japan, in this photo taken by Kyodo July 7, 2018.
As the death toll continued to climb from the rainfall, which began earlier this week, Okayama prefecture said a man caught in a landslide was pronounced dead.
The body of a woman was found by a river in central Japan's Gifu while a 59-year-old man was confirmed dead after being found by a river in western Hiroshima prefecture, local police said.
A vehicle was retrieved from a swollen river in the early hours of Friday morning, believed to be that of a woman in her 50s who went missing after leaving her home in Kyoto Prefecture.
Among the missing were five people who got buried when housing collapsed, also in Hiroshima prefecture.
"This is heavy rain at a level we've never experienced", a JMA official said as the agency issued warnings in Okayama, Hiroshima, Tottori, Fukuoka, Saga, Nagasaki, Hyogo and Kyoto prefectures on July 6.
The agency said that, although a weather front had settled between western and eastern Japan, there was a risk that heavy rains would continue as warm air flowed towards the front. Several train routes were also closed.
The "historic" rainfall will keep battering saturated parts of Japan through Sunday, Japan's Meteorological Agency said.
The two deaths were on the main island of Honshu, according to Reuters. "In fear of heavier downpours, we've issued emergency warnings in areas where the amount of rain hasn't exceeded the standards of such a warning system", a JMA official explained.