Unprecedented rain in Japan unleashed heavy floods on Thursday that tore houses from their foundations, uprooted trees and forced more than 100,000 people from their homes.

Helicopters hovering over swirling, muddy waters rescued many people from the roofs of their homes. Two people were missing and at least 17 were injured.

As heavy rain pummeled Japan for a second straight day, the Kinugawa River broke through a flood berm at 12:50 pm, sending water gushing into the eastern half of Joso, a city of 60,000 people about 50 kilometers northeast of Tokyo.

Aerial footage showed a wide swath of the city underwater, more than one story deep in some places. The rains came on the heels of Tropical Storm Etau, which caused flooding and landslides elsewhere on Wednesday as it crossed central Japan.

Some areas received double the usual September rainfall in 48 hours after Etau swept across Japan's main island of Honshu.

A 63-year-old woman was missing in a landslide that hit her home, while a man in his 70s in Joso was feared trapped when water engulfed his home, NHK national television said.

"We heard a huge sound like a thunderclap, and then the hillside came down," a man told NHK, referring to the landslide that swept away his neighbor.

Television broadcast footage of helicopters winching people to safety, including an elderly couple clutching a pair of struggling dogs as the flood tore away pieces of their home.

A further 800,000 people were at one point advised to evacuate after officials issued predawn warnings of "once in a half-century rains" to 5 million people in areas east and north of Tokyo.

Japan has put heavy emphasis on disaster prevention since a 2011 earthquake and tsunami killed nearly 20,000 people and authorities are keen to avoid criticism for what was seen as a sluggish response.

Prime Minister Shinzo Abe warned of more rain and said he was setting up an emergency center.

"The government will work as one to prioritize the safety of the people and do our best to prevent any further disaster," Abe told reporters.

Television footage showed people in Joso waving towels while waiting for help on the upper floors of homes engulfed in floods after the overflowing Kinugawa River swept through.

"I thought I was safe because I live on a hill, but pretty soon the water came up and everything was washed away," a barefoot man told Fuji TV after his helicopter rescue.

Up to 12 military helicopters took part in the rescue along with an initial 55 members of Japan's military. Officials said the numbers would rise.

The Transport Ministry estimated that up to 6,900 households in a 37-square-km area could be affected by the flooding, the Kyodo News Agency said.

Rescue workers rushed to find people before nightfall. Part of a hotel in Nikko, famed for its shrines and temples, collapsed, Kyodo said, but there were no reports of injuries.

Rainfall reached 500 mm around Joso, NHK said, with weather officials expecting at least 200 mm more in parts of eastern Japan.

Reuters - AP

Flooding victims wait for rescue helicopters in a residential area flooded by the Kinugawa River in Joso, Ibaraki prefecture, Japan, on Thursday. Two people were missing and 800,000 were advised to evacuate after rivers burst their banks north of Tokyo following days of heavy rain. Kyodo / Reuters