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 U.S. Geological Survey said the magnitude 5.3 quake was centered in the ocean off the coast of Chiba, near Tokyo, and was fairly deep, at 59.5 kilometers (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.
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 center wasn't 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 162 kilometers (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, 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 neighborhoods 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.
Yusuke Ikegaya, a Shizuoka resident who evacuated ahead of the storm, said he was surprised that the nearby river was about to overflow in the morning, hours before the typhoon made landfall.
"In the 28 years of my life, this is the first time I've had to evacuate even before a typhoon has landed," he said.
Authorities also warned of mudslides, common in mountainous Japan.
Public broadcaster NHK said Shiroyama dam in Kanagawa prefecture, also southwest 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 canceled, 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.
Residents taped up their apartment windows to prevent them from shattering. TV talks shows showed footage of household items like a slipper bashing through glass when hurled by winds.
Evacuation advisories were issued for risk areas, including Shimoda city, west of Tokyo. Dozens of evacuation centers were set up in coastal towns, and people rested on gymnasium floors, saying they hoped 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 to Sunday. The Defense Ministry cut a three-day annual navy review to a single day on Monday.
All Nippon Airways and Japan Airlines grounded most domestic and international flights at the Tokyo, Osaka and Nagoya airports. Central Japan Railway Co. canceled bullet-train service between Tokyo and Osaka except for several early Saturday trains connecting Nagoya and Osaka. Tokyo Disneyland was closed, while Ginza department stores and smaller shops throughout Tokyo were shuttered.
A typhoon that hit the Tokyo region in 1958 left more than 1,200 people dead and half a million houses flooded.