At least two people have been killed and 18 others are missing in huge floods that are surging through southern Japan, with authorities warning hundreds of thousands of people to flee.

Unprecedented torrential rain has caused rivers to burst their banks, sweeping away roads and houses, and destroying schools.

Thousands of soldiers and other rescuer workers were scrambling Thursday to reach people cut off by torrents of swirling water or threatened by landslides, as forecasters warned of worse to come.

"We are in an extremely serious situation," Deputy Prime Minister Taro Aso said, warning of the danger of collapsing hillsides and adding "many people are still missing".

More than 50 centimetres (20 inches) of rain deluged parts of Kyushu, the southernmost of Japan's four main islands, over 12 hours on Wednesday, the meteorological agency said.

Downpours will likely continue through Friday, the agency said as the region grapples with the aftermath of a typhoon that raked the country this week.

Authorities lifted "special" heavy rain warnings for the hardest hit prefectures of Fukuoka and Oita, although lesser warnings remained in place.

Japan is deploying 7,500 police, rescue personnel and troops in affected areas of Kyushu, Chief Cabinet Secretary Yoshihide Suga said.

"There is a lot of information about people who are unaccounted for," he told a press conference, declining to confirm the number of people missing.

Those included a child reportedly carried off by a fast-flowing river and a couple who had not been seen since their house was swept away.

A man was found dead in the city of Asakura in Fukuoka prefecture, public broadcaster NHK and Jiji Press reported, citing police sources.

NHK and Jiji also reported that a man died in a landslide in Hita, in Oita prefecture, but an official there could not immediately confirm it.

Local officials said in total they knew of 18 people who were missing in Fukuoka and Oita.

- 'Hang in there!' -

Television footage showed rolling waves from swollen rivers hitting residential areas, tearing up roads and inundating farmland.

Asakura was among the hardest hit with footage showing floodwaters surging through the streets.

Ryoichi Nishioka, who grows flowers in the city, said he tried to save them from damage amid fast rising waters the night before.

"I tried to protect them by covering them up but couldn't make it," he told AFP. "Then the swirling water flooded this area and swept away the greenhouses."

Nishioka, 67, also described helping a man who clung to an electric pole as muddy waters rampaged through the area.

"We had a blackout, so I used a flashlight from the second floor and put light for him," he said. "I was calling out to encourage him for three hours from 9pm to midnight.

"I shouted: 'Hang in there!'" The man was ultimately rescued, Nishioka said.

An elderly man in the hard-hit Haki district of Asakura told NHK how furniture bobbed in the flood waters that inundated his home.

"I dodged them and escaped in a gush of water," he said.

A railroad bridge has been destroyed by the raging Kagetsu river, disrupting train services, a railway spokesman said.

Several other train lines were also forced to delay or stop operations due to heavy rains, while local officials called off classes at primary and middle schools.

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