Rescue efforts for people stranded in flooded areas are in full force today after Typhoon Haibis dashed heavy rainfall and winds through a widespread area of Japan, including Tokyo.

Hagibis made landfall south of Tokyo on Saturday and moved northward.

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The typhoon left four people dead, 17 missing and more than 100 people injured, according to public broadcaster NHK.

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The numbers were growing, underlining the damage from Hagibis, which means "speed" in the Philippine language of Tagalog.

News footage showed a rescue helicopter hovering in a flooded area in Nagano Prefecture, after an embankment of the Chikuma River broke, plucking people from the second floor of a home submerged in muddy waters.

Several other rivers had also overflowed, including Tama River near Tokyo, according to NHK.

Authorities warned that the risk of mudslides remained.

Some train services in the Tokyo area, much of which had halted, resumed from early morning, although others were undergoing safety checks and were expected to start later in the day.

The World Rugby Cup match between Namibia and Canada, scheduled for Sunday in Kamaishi, northern Japan, was canceled as a precautionary measure for safety reasons.

Matches on Saturday - including the All Blacks v Italy clash - we cancelled.

Stores and amusement parks had been closed.

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The usually crowded train stations and streets of Tokyo were abandoned as people were advised to stay indoors.

But life was quickly returning to normal under clear sunny skies.

About 17,000 police and military troops had been standing ready for rescue operations, under government orders.

Evacuation centers had been set up in coastal towns, and tens of thousands of people had evacuated, praying their homes were still there after the storm passed.

The typhoon disrupted a three-day weekend in Japan that includes Sports Day on Monday.

Qualifying for a Formula One auto race in Suzuka was pushed from Saturday to Sunday.

The authorities had repeatedly warned Hagibis was on par with a typhoon that hit the Tokyo region in 1958. But the safety benefits that Japan's modernszation had brought were apparent. The typhoon six decades ago had left more than 1200 people dead and half a million houses flooded.

EARLIER REPORT:

At least six million people were told to evacuate their homes as Super Typhoon Hagibis smashed into Japan on Saturday, triggering mudslides, flooding and the heaviest rain and winds in 60 years.

Within hours of the typhoon making landfall at around 7pm local time, at least two people were dead, nine were missing and more than 80 were injured, according to local media.

Officials warned that the storm could be the most powerful to hit Japan since one of the worst typhoons on record devastated Tokyo and surrounding areas in 1958, killing more than 1200 people.

Even before the storm hit, there were reports of at least one death, with a 50-year-old man killed when his car overturned in strong winds in Chiba Prefecture, an area just east of Tokyo still recovering from a strong typhoon which hit last month. Four others, including two children, were also injured by a tornado in the same area.

One resident there told NHK: "When the winds suddenly hit, they blew the roof off my house. The noise was awful. One of my three children was injured but is now in a hospital."

The typhoon had been brewing over the Pacific Ocean with recorded winds of more than 233kmh. Authorities issued warnings that with gusts likely to exceed that figure, some houses were at risk of being blown down.

Tokyo station entrance is deserted in Tokyo, as Typhoon Hagibis approaches. Photo / AP
Tokyo station entrance is deserted in Tokyo, as Typhoon Hagibis approaches. Photo / AP

The Japan Meteorological Agency warned of as much as 76cm of rain in the 24-hour period until midnight on Saturday.

Television footage showed images of damage to roofs and walls of buildings in storm-hit spots across Japan. More than 16,000 homes, mainly along the Pacific coastline, were without electricity.

Some residential areas along the coast in Shizuoka were also reported as being submerged up to around knee height in tidal surges. The approaching typhoon caused rivers to overflow in the area, with reports of at least one person swept away, and widespread landslide warnings also in place.

Japan team's Michael Leitch works out, ahead of their Rugby World Cup Pool A match against Scotland as Typhoon Hagibis approached. Photo / AP
Japan team's Michael Leitch works out, ahead of their Rugby World Cup Pool A match against Scotland as Typhoon Hagibis approached. Photo / AP

Three people were missing in Gunma Prefecture after a landslide swept through six houses.

The weather system passed directly over Tokyo, one of seven regions subject to the non-compulsory evacuation orders - and where a 5.7 magnitude earthquake hit just ahead of the typhoon's arrival. Around 17,000 Self-Defence Forces personnel were on standby across the country for potential deployment on rescue operations.

Even as the typhoon moved away from the capital late on Saturday, one expert warned of further flooding as several surrounding prefectures began releasing water from dams, letting it flow downstream.

Cars sit submerged in water in the residential area hit by Typhoon Hagibis, in Ise, central Japan yesterday. Photo / AP
Cars sit submerged in water in the residential area hit by Typhoon Hagibis, in Ise, central Japan yesterday. Photo / AP

"The situation is now worse than this evening," Nobuyuki Tsuchiya, director of the Japan Riverfront Research Centre, told Reuters. About 1.5 million people in Tokyo live below sea level.

A study by the Japan Society of Civil Engineers in June 2018 concluded that a huge storm surge in Tokyo Bay could lead to 8000 deaths and cause damage estimated at Y115 trillion ($168 billion).

Much of the damage would be to infrastructure, such as underground railway lines, roads and bridges, as well as structures on vulnerable reclaimed land in the bay.

A disaster simulation prepared by the Tokyo Metropolitan Government in 2018 suggested that more than 207sq km of the city could be inundated in a worst-case scenario, accounting for one-third of the entire city. In low-lying areas, water levels could rise as high as 9.7m above mean sea level.

The government's estimations are based on data from Typhoon Muroto, which struck the city in September 1934, killing 3066 people, injuring a further 13,000 and leaving 200,000 people homeless.

Rescuers on a boat patrol the residential area flooded by Typhoon Hagibis, in Ise, central Japan. At least six million people have been told to evacuate. Photo / AP
Rescuers on a boat patrol the residential area flooded by Typhoon Hagibis, in Ise, central Japan. At least six million people have been told to evacuate. Photo / AP

Authorities in central Japan called on residents of coastal regions to evacuate to higher ground inland and alerts were sent out to mobile phones through messaging systems and are running on television and radio broadcasts.

Train services in and around Tokyo were cancelled throughout Saturday, along with long-distance bullet train services. Japanese airlines grounded all domestic and international flights out of Narita and Haneda, the two airports that serve the capital, while theme parks and many shops closed their doors.

A number of companies, including car makers Toyota and Honda, have halted production.

Saturday's Rugby World Cup game between England and France in Yokohama has been cancelled, along with the Italy-New Zealand clash in Toyota City.

A decision is due to be made at midnight on games scheduled for Sunday, including the all-important Scotland-Japan game, which will decide which nation emerges from the group stages of the tournament.

The looming super typhoon has also triggered a frenzy of last-minute buying, with store shelves emptied of bread, instant noodles, bottled water and other perishable foods. Stores in some areas have also reportedly run out of batteries and packing tape that is being put across windows to reduce the possibility of flying glass.

Super Typhoon Hagibis - the Tagalog word for "speed" - is the second major storm to hit Japan in just over a month.

Typhoon Faxai struck eastern Japan on September 9, killing three people, leaving more than 40 injured and leaving scenes of devastation in its wake. At the peak of the storm, more than 930,000 people were without power and it took two weeks for some areas to have electricity restored.