The typhoon disaster is frightening and residents are faced with uncertainty.
Flights are cancelled and train services suspended as the country braces for the heaviest rain and winds seen in 60 years.
Typhoon Hagibis has made landfall in Japan, with strong winds and a heavy downpour battering Shizouka, southwest of Tokyo.
About six million people in Japan have been advised to leave their homes as strong winds and rains picked up before the typhoon even arrived.
An earthquake measuring 5.3, according to the US Geological Survey, shook the areas which had been drenched by rainfall. The earthquake was in the ocean off Chiba, near Tokyo.
A man in his forties was killed after his car overturned in a tornado east of Tokyo, while five others were injured as gales tore the roofs off a number of houses, before the storm made landfall.
Once the typhoon arrived, it injured 60 people, bringing the heaviest rain and winds seen by Japan in 60 years. There are warnings of floods and landslides.
Several people are missing in a town near Tokyo after a landslide destroyed two houses.
It comes after one of the strongest typhoons to hit the country in recent years destroyed or damaged 30,000 houses and caused extensive power cuts.
The latest storm has already led more than 16,000 households to lose power, while shops, factories and subways have been shut down as a precaution.
Organisers of the Japanese Formula One Grand Prix have cancelled all practice and qualifying sessions, while two matches of the Rugby World Cuphave also been scratched.
England’s match against France was cancelled, and the team has returned to Miyazaki where they held their pre-tournament training camp. New Zealand’s match against Italy was also cancelled.
Japan’s rugby team had to wade through high waters to get to their sodden pitch for practice, as their match against Scotland on Sunday could still go ahead if organisers believe it is safe.
World Rugby told fans of Namibia and Canada not to travel to Kamashi ahead of Sunday’s planned match, as they consider whether it should be cancelled. The teams have also been advised of potential cancellation.
More than 1,600 flights have been cancelled and train services suspended.
Tokyo Disneyland was also closed.
Some 17,000 police and military troops have been called up, standing ready for rescue operations, while dozens of evacuation centres have opened in coastal towns.
Hagibis, which means speed in Filipino, is expected to make landfall near Tokyo later, dumping up to 50cm (20ins) of rain.
Yasushi Kajihara, from Japan’s meteorological agency, said: “Be ready for rainfall of the kind that you have never experienced. Take all measures necessary to save your life.”
Evacuation centres have opened, with people taking refuge on floors and hoping their homes would be there when they return.
Yuka Ikemura, a 24-year-old nursery school teacher, is in an evacuation centre in Tokyo with her three-year-old son, eight-month-old daughter, and their pet rabbit.
She said: “I’ve got small children to take care of and we live on the first floor of an old apartment.”
“We brought with us the bare necessities. I’m scared to think about when we will have run out diapers and milk.”
A typhoon that hit the Tokyo region in 1958 left more than 1,200 people dead and half a million houses flooded.