Public broadcaster NHK gave a higher toll than the government of 10 dead and 16 missing plus 128 injured as more details were coming in the from field, a day after Typhoon Hagibis made landfall south of Tokyo and moved northward.
"The major typhoon has caused immense damage far and wide in eastern Japan," government spokesman Yoshihide Suga told reporters, adding that 27,000 military troops and other rescue crews were deployed for the operation.
News footage showed a rescue helicopter hovering in a flooded area in Nagano prefecture where an embankment of the Chikuma River broke, and streams of water were continuing to spread over residential areas. The chopper plucked those stranded on the second floor of a home submerged in muddy waters.
Aerial footage showed tractors at work trying to control the flooding. Meanwhile, rows of Japan's prized bullet trains, parked in a facility, were sitting in a pool of water.
A stretch of Fukushima, in the city of Date, was also flooded with only rooftops of residential homes visible in some areas. Parts of nearby Miyagi prefecture were also under water.
The Tama River, which runs by Tokyo, overflowed its banks.
Authorities warned of a risk of mudslides. Among the reported deaths were those whose homes were buried in landslides. Other fatalities included people who got swept away by raging rivers.
Suga said that damage to housing from the flooding was extensive but promised recovery was on its way. Some 376,000 homes were without electricity, and 14,000 homes lacked running water, he said.
Boats as well as helicopters were sent to the flooded areas, while rescue crew dug through dirt in other areas to try to get people out from homes buried by landslides.
Several train service in the Tokyo area resumed early morning, although others were undergoing safety checks and were expected to restart later Sunday.
Ruling party politician Fumio Kishida said the government will do its utmost in rescue operations, including making sure that those who moved to shelters were taken care of.
He acknowledged Japan's power grids need to be strengthened so people in disaster areas can rely on timely information.
"So many risks remain, and it is a reality we must stay on guard," Kishida said on an NHK TV news talk show. "We must do our utmost. In these times, a disaster can hit anytime."
The Rugby World Cup match between Namibia and Canada, scheduled for Sunday in Kamaishi, northern Japan, was canceled as a precautionary measure, but organizers announced Japan will play Scotland as scheduled Sunday evening.
All matches on Saturday had been canceled, and stores and amusement parks closed.
As the typhoon bore down on Saturday with heavy rains and strong winds, the usually crowded train stations and streets of Tokyo were deserted with people advised to stay indoors. But life was quickly returning to normal under crisp clear skies Sunday.
Evacuation centers had been set up in coastal towns with tens of thousands seeking shelter. Kyodo News service said evacuation warnings had been issued to more than 6 million people.
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 infrastructure that Japan's modernization had brought was apparent. The typhoon six decades ago had left more than 1,200 people dead and half a million houses flooded.