The Meteorological Agency says more heavy rain is expected in eastern and western Japan, and people should remain on the alert for landslides and flooding.
Some rivers in Iwate Prefecture are at risk of overflowing.
The agency says a front, accompanied by low pressure systems, created unstable atmospheric conditions from western to northern Japan, with rain over wide areas on Sunday.
A low pressure system above the Yellow Sea will move over the Sea of Japan through Tuesday, bringing more rain in western and eastern Japan with thunderstorms in some areas.
In areas affected by heavy rain, the ground has become loose and river dikes have been damaged. Even a small amount of rain could trigger disasters.
Weather officials are urging people to stay on the alert for landslides, overflowing rivers and flooding in low-lying areas.