At least 45 people are missing as torrential rains that have killed 11 people pounded western and central Japan, public broadcaster NHK has reported, with more than 1.6 million people forced from their homes.

Japan's Meteorological Agency issued special weather warnings across four prefectures in the west of Japan's main island of Honshu, urging vigilance against landslides, rising rivers and strong wind amid what it called "historic" rain.

The agency said that, although a weather front had settled between western and eastern Japan, there was a risk heavy rains would continue as warm air flowed towards the front.

Areas already saturated faced more rain on Sunday, it said.

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.

Two other people were feared dead after being found in buildings hit by landslides, NHK said.

One, a 95-year-old woman, was found in her house after part of a nearby mountain collapsed.

The previous death toll had been put at four on Friday.

Chief Cabinet Secretary Yoshihide Suga said about 48,000 police, firefighters and members of Japan's Self-Defence Forces were responding to more than 100 landslides and other appeals for help.

By Saturday morning, more than 1.6 million people were ordered to leave their homes amid fears of flooding and further landslides, with a further 3.1 million advised to leave, the Fire and Disaster Management Agency said.

In Motoyama, a town in Shikoku island, 583mm of rain fell in the 24 hours between Friday and Saturday mornings, the Meteorological Agency said.

Some transport was affected in the southernmost main island of Kyushu.

Wide parts of the expressway were covered with soil and landslide debris in the north of the island, the Kyodo news agency reported.