Torrential rains has pounded some parts of western Japan with three times the amount normally seen in July.
The death toll from torrential rain and landslides in western Japan rose to 81 people on Sunday, with dozens still missing after more than 2,000, temporarily stranded in the city of Kurashiki, were
Evacuation orders were in place for nearly 2 million people and landslide warnings were issued in many prefectures.
In hard-hit western Japan, emergency services and military personnel used helicopters and boats to rescue people from swollen rivers and buildings, including a hospital.
Scores of staff and patients, some still in their pajamas, were rescued from the isolated Mabi Memorial Hospital in boats rowed by members of Japan's Self Defence Forces.
A city official said 170 patients and staff had been evacuated while public broadcaster NHK later said about 80 people were still stranded.
Torrential rains pounded some parts of western Japan with three times the amount normally seen in July.
The government has set up an emergency management centre at the prime minister's office.
"Even now we have not been able to confirm the safety of quite a lot of people, and there are many who are stranded, facing the terror of impending inundation and waiting for rescue," prime minister Shinzo Abe said.
Much of the country outside major cities is mountainous and building takes place on virtually every bit of usable land and that has left Japan vulnerable to disasters.
Emergency warnings remain in three prefectures, with 300 mm predicted to fall by Monday morning in parts of the smallest main island of Shikoku.