Heavy rain and strong winds pounded Tokyo as a powerful typhoon forecast to be Japan's worst in six decades made landfall.
Store shelves were bare after people stocked up on water and food ahead of Typhoon Hagibis.
The Japan Meteorological Agency warned of dangerously heavy rainfall in Tokyo and surrounding prefectures, including Gunma, Saitama and Kanagawa.
An earthquake shook the area drenched by the rainfall shortly before the typhoon made landfall in Shizuoka prefecture on Saturday evening.
The US Geological Survey said the magnitude 5.3 quake was centred in the ocean off the coast of Chiba, near Tokyo, and was fairly deep, at 37 miles. Deep quakes tend to cause less damage than shallow ones.
"Be ready for rainfall of the kind that you have never experienced," said meteorological agency official Yasushi Kajihara, adding that areas usually safe from disasters may prove vulnerable.
"Take all measures necessary to save your life," he said.
Mr Kajihara said people who live near rivers must take shelter on the second floor or higher of any sturdy building if an officially designated evacuation centre was not easily accessible.
He also expressed fears that disaster may have already struck in some areas.
Hagibis, which means "speed" in Filipino, was advancing north-northwestward with maximum sustained winds of 100 miles per hour, according to the meteorological agency.
The storm brought heavy rainfall in wide areas of Japan all day ahead of its landfall, including in Shizuoka and Mie prefectures, southwest of Tokyo, as well as Chiba to the north, which saw power outages and damaged homes in a typhoon last month.
Under gloomy skies, a tornado ripped through Chiba on Saturday, overturning a car in the city of Ichihara and killing a man inside the vehicle, city official Tatsuya Sakamaki said.
Five people were injured when the tornado ripped through a house. Their injuries were not life-threatening, Mr Sakamaki said.
The heavy rain caused rivers to swell, flipped anchored boats and whipped up sea waters in a dangerous surge along the coast, flooding some residential neighbourhoods and leaving people to wade in ankle-deep waters and cars floating.
In Shizuoka, one of two men who went missing in the Nishikawa River was rescued, Gotemba city official Fumihiko Katsumata said.
Firefighters said the two men were working at a river canal to try to control overflowing when they were swept away.
Authorities also warned of mudslides, common in mountainous Japan.
Public broadcaster NHK said Shiroyama dam in Kanagawa prefecture, also south-west of Tokyo, may release some of its waters, which were nearing limits.
An overflooded dam is likely to cause greater damage, and so releasing some water gradually is a standard emergency measure.
Rugby World Cup matches, concerts and other events in the area were cancelled, while flights were grounded and train services halted.
Authorities acted quickly, with warnings issued earlier in the week, including urging people to stay indoors.
Some 17,000 police and military troops were called up, standing ready for rescue operations.