Weather officials are warning that thunderstorms may hit eastern and western Japan through Saturday.
The Meteorological Agency says atmospheric conditions are unstable mainly in eastern Japan, as warm, damp air is pouring into a rain front and a low-pressure system.
Rain intensified mainly in western Japan until early hours of Friday. In Matsuyama City, Ehime Prefecture, the rainfall from Wednesday to 4 a.m. on Friday reached nearly 90 percent of the monthly average for July. A mudslide in the city has left three people unaccounted for.
The rain front is expected to stay over the Pacific side of the country from western to eastern Japan through Saturday.
Localized thunderstorms are likely along the Pacific coast in eastern Japan through late Friday night and in western Japan through Saturday.
The maximum rainfall in the 24 hours until Saturday evening is expected to be 120 millimeters in southern Kyushu, and 80 millimeters in northern Kyushu, Shikoku and Kinki regions.
The ground has loosened in areas hit by heavy rain. Additional rain could raise the risk of disaster.
The agency is urging people to be on alert for landslides, flooding in low-lying areas and swollen rivers along with lightning strikes, gusts, tornadoes and hail.
When developed thunderclouds are approaching, people are advised to take shelter in sturdy buildings.