Police told The Yomiuri Shimbun Sunday 10,000 residents in the town of Minami-Sanrikucho and another 10,000 in Otsuchicho were missing after Friday's earthquake and tsunami.
The head of the Miyagi prefectural police said the number of deaths in his province alone would "no doubt be tens of thousands."
Government functions in six towns on the northeastern coast were knocked out, making the full extent of damage unknown, emergency officials said.
The military said more than 20,000 people were stranded and pleading for rescue in Miyagi prefecture.
The government estimated 46,000 buildings were damaged; 5,700 of those collapsed entirely or were washed away by the floodwaters, most of them in Iwate prefecture, NHK reported.
The National Police Agency said bridges and roads were damaged in at least 600 places across 11 prefectures, while 66 landslides were recorded in seven prefectures.
Saying Japan faced its greatest crisis since World War II, Prime Minister Naoto Kan took the extraordinary step of ordering power cuts to avert a nationwide blackout, Kyodo News reported.
As authorities struggled to avert a meltdown at the Fukushima nuclear power plant, a state of emergency was declared at another nuclear complex plant in Onagawa, where excessive radiation levels were recorded, the United Nations' atomic watchdog agency told CNN.
Around Fukushima, at least 200,000 people have now been evacuated, the Los Angeles Times reported.
The Asahi Shimbun newspaper said at least 70 atomic workers were exposed to heavy radiation levels as a result of an explosion at one reactor site. Two other reactors were in danger of overheating as a result of the earthquake and the loss of cooling abilities, officials said.
Chief Cabinet Secretary Yukio Edano told reporters there were concerns of an atomic core meltdown, as happened in Chernobyl in 1986 in Ukraine.
"We can't rule out the possibility of a blast," Edano said.
The Japan Meteorological Agency upgraded the magnitude of Friday's quake to 9.0 from the original 8.9 estimate. While the country has been experiencing numerous aftershocks, the JMA warned there was a 70 percent probability of a magnitude-7 quake in the next three days.
The government mobilized its largest post-war deployment of national guard and military members into service, with about 100,000 troops fanning out to devastated regions, The New York Times reported.
The U.S. aircraft carrier USS Ronald Reagan has started delivering aid on the coast. Crew members, working with the Japanese navy, have carried out 20 sorties delivering aid pallets by helicopter, the U.S. military said Sunday.
Residents of Sendai reported unbelievable devastation. Whole areas of the town were washed away.
"I've been watching TV, but it looks much worse when I actually see it in person," one witness told CNN.
Tokyo was beginning to return to normal, CNN reported, but the persistent aftershocks had everyone on edge. Supermarkets were cleaned out of basic foods.