Raging floodwaters broke through an embankment Thursday and swamped a city near Tokyo, washing away houses, forcing dozens of people to rooftops to await helicopter rescues and leaving one man clinging for his life to a utility pole.

There were no immediate reports of casualties, but rescue officials said they were overwhelmed by pleas for help. More than 30,000 were ordered to flee their homes, and hundreds more were stranded by the water. As of late Thursday, more than 3,500 people were staying in evacuation centres.

An earlier report from Reuters indicated as many as 100,000 had been forced from their homes due to flooding.

As heavy rain pummeled Japan for a second straight day, the Kinugawa River broke through a flood berm, sending water gushing into the eastern half of Joso, a city of 60,000 people about 50 kilometres northeast of Tokyo.

'It almost looked like a tsunami'

Aerial videos showed a wide swath of cityscape underwater, more than one storey deep in some places. The rains came on the heels of tropical storm Etau, which caused flooding and landslides elsewhere Wednesday as it crossed central Japan.

Yuko Kawamoto, 58, said she decided to leave her home with her 80-year-old mother after watching TV images of the water pouring out of the embankment. "It almost looked like a tsunami," she said.

She said the muddy water was ankle-deep when they left their house, carrying duffel bags and an umbrella each, and was almost up to their hips when they reached the evacuation centre.

Japanese broadcasters showed live video of rescuers being lowered from helicopters and clambering onto second-floor balconies to reach stranded residents.

In one dramatic scene, a rescuer descended four times from a military helicopter over 20 minutes to lift up four people one by one as a deluge of water swept around their home.

Nearby, a man clung to a utility pole as the waters rose. He was taken up by a rescue worker who had to be first lowered into the rushing water so he could make his way over to the man.

Others waved cloths from their decks or roofs to get attention as torrents of water washed away cars and knocked over buildings. Photos from Japan's Kyodo News service showed people waiting for help on top of cars and a 7-Eleven delivery truck, surrounded by water that nearly submerged the cars.

Japan flood

Rescue crews were trying to get to people stranded on rooftops as flooding continued in Joso, Ibaraki Prefecture. (jiji Press/AFP/Getty Images)

Muddy water was still rising late Thursday on a street heading to Joso City Hall, and police were blocking traffic in that direction.

Akira Motokawa, a city evacuation official, told public broadcaster NHK that rescuers have been unable to keep up with the volume of calls for help.

As of Thursday evening, nine people were possibly missing because authorities could not reach them, city official Takao Kobayashi said. Authorities had rescued 70 of the 176 people who had requested help. Another 100 people were reported trapped on the second floor of a flooded supermarket, and 80 more in a nursing home.

A total of 3,580 people in the affected 37-square kilometre area were sheltered at schools, community centres and other safer areas. Military troops were delivering food, blankets and water to about 780 people in several communities who were stranded but not seeking rescue.

Dozens of residents had evacuated to City Hall, carrying small bags of personal items. They rested in conference rooms, and a waiting area on the first floor was opened for them to stay overnight.

Soldiers in camouflage uniforms and helmets rushed around, while wet uniforms and raingear hung from chairs to dry.

Tokyo was drenched with rain, but the hardest-hit area was to the north in Ibaraki and Tochigi prefectures. One woman was missing hours after a landslide hit houses at the foot of a steep, wooded incline. High-speed "bullet" train service was partially suspended.

The Fire and Disaster and Management Agency said 22 people have been injured by the storms over the past two days, including three elderly women who were seriously hurt when strong winds knocked them over.