At least 58 people have died in several days of flooding.

By Wednesday morning, parts of Nagano and Gifu in central Japan were flooded by massive downpours.

Footage on NHK television showed swollen water in the Hida River gouging into the embankment, destroying a national highway along the river.

In another central Japanese city of Gero, river water rose to just below the bridge above it.

In a mountainous town of Takayama, several houses were hit by a mudslide, with uprooted trees and other debris scattered around. It was not immediately known what happened to their residents.

Across the country, about 3.6 million people were advised to leave, although evacuation is not mandatory and the number of people who actually took shelter was not provided.

As of Wednesday morning, the death toll from the heavy rains starting at the weekend had risen to 58, most of them from the hardest-hit Kumamoto prefecture.

Four others were found in Fukuoka, another prefecture on Kyushu, Japan's third-largest island.

Though the rains were causing fresh flooding threats in central Japan, flooding was still affecting the southern region. And search and rescue operations continued in Kumamoto, where 14 people are still missing.

Tens of thousands of army troops, police and other rescue workers mobilised from around the country to help and the rescue operations have been hampered by the rains, flooding, mudslides and disrupted communications.

Australian Associated Press