Torrential rain that caused deadly floods in southern Japan was moving north-east on Wednesday, battering large areas of Japan’s main island, swelling more rivers, triggering mudslides and destroying houses and roads.

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

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

Japan Floods
The playground of a junior school in Gero, Gifu prefecture, southern Japan was flooded (Kyodo News/AP)

Footage on NHK television showed a swollen river gouging into the embankment, destroying a highway, while in the city of Gero, the rising river was flowing just below a bridge.

In the mountainous town of Takayama, several houses were hit by a mudslide, their residents all safely rescued.

In Kagoshima, a pick-up truck was hit by a mudslide and fell into the sea, but the driver was airlifted out with a head injury, according to Fuji Television.

In another town in Oita, two brothers in their 80s were dug out alive by rescuers after a mudslide smashed into their hillside house, NHK said.

Japan Floods
A man walks through a flooded road following heavy rain in Omuta, Fukuoka prefecture, southern Japan (Juntaro Yokoyama/Kyodo News/AP)

As of Wednesday morning, the death toll from the heavy rain which started over 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.

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

Rain had subsided by Wednesday afternoon in many areas, where residents were busy cleaning up their homes and work places.

Japan Floods
A vehicle and a tree lie down following a heavy rain in Hita, Oita prefecture, southern Japan (Kyodo News/AP)

In Gero, a man washed down mud at the entrance of his riverside house despite the evacuation advice.

“I was told to run away and my neighbours all went, but I stayed,” he said. “I didn’t want my house to be washed away in my absence.”

In Oita, teachers at a nursery school were wiping the floor and drying the wet furniture.

“I hope we can return to normal life as soon as possible,” Principal Yuko Kitaguchi told NHK.

Though the rain was causing fresh flooding threats in central Japan, floods were 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 assist, and the rescue operations have been hampered by the rains, flooding, mudslides and disrupted communications.

Japan Floods
The heavy rain damaged a road in Hita, Oita prefecture, southern Japan (Miyuki Saito/Kyodo News/AP)

Chief Cabinet Secretary Yoshihide Suga urged residents to use caution.

“Disasters may happen even with little rain where grounds have loosened from previous rainfalls,” he said.

Mr Suga pledged continuing search and rescue efforts, as well as the government:s emergency funds for the affected areas.

Japan is at high risk of heavy rain in early summer when wet and warm air from the East China Sea flows into a seasonal rain front above the country.

In July 2018, more than 200 people, about half of them in Hiroshima, died from heavy rain and flooding in south=western Japan.