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The 8.9-magnitude tremor unleashed a monster 10-metre (33-foot) tsunami that raced over towns and farming land, destroying all before it and leaving the coast a swampy wasteland.
In the small port town of Minamisanriku alone some 10,000 people were unaccounted for -- more than half the population -- public broadcaster NHK reported.
Police and military reported finding groups of hundreds of bodies at locations along the shattered coastline, including more than 200 found at a new site on Sunday.
The top government spokesman said at least 1,000 people were believed to have lost their lives, and police said more than 215,000 people were huddled in emergency shelters.
As the world's third-largest economy struggled to assess the full extent of what Prime Minister Naoto Kan called an "unprecedented national disaster", it faced an escalating atomic emergency.
In the city of Fukushima, about 80 kilometres (50 miles) northwest of the plant, AFP reporters saw panic buying at supermarkets and said petrol stations had run dry.
At the Fukushima No. 1 atomic plant 250 kilometres (160 miles) northeast of Tokyo, the quake knocked out cooling systems vital for keeping the reactor from overheating, and back-up generators were disabled by tsunami flooding.
Smoke billowed into the sky Saturday as a blast destroyed the building around one of the reactors. The government moved to calm growing fears, saying the explosion did not rupture the container surrounding the reactor itself.
Workers doused the stricken No.1 reactor with sea water to try to avert catastrophe, but the situation deteriorated and the plant operator said another reactor at the quake-hit facility was also in trouble.
"All the functions to keep cooling water levels in No. 3 reactor have failed at the Fukushima No. 1 plant," operator TEPCO said, adding that pressure was rising slightly.
Kyodo reported that the fuel rods at one reactor were now three metres above the water, and that a radiation leak believed to be from the reactor itself had now reached levels above the legal limit.
Japan's ambassador to the United States Ichiro Fujisaki told CNN: "There was a partial melt of a fuel rod, melting of fuel rod. There was a part of that... but it was nothing like a whole reactor melting down."
Japan's nuclear safety agency rated the incident at four on the international scale of zero to seven. The 1979 Three Mile Island accident in the United States was rated five, while the 1986 Chernobyl disaster was a seven.
The International Atomic Energy Agency said about 200,000 people had so far been evacuated from the area around the two Fukushima plants. There are a total of 10 reactors at the two plants.
Media reports said three residents -- bedridden patients evacuated from a hospital near the No. 1 plant -- had been found to be exposed to radiation after spending a long time outdoors awaiting rescue.
US nuclear experts warned that pumping sea water to cool the reactor was an "act of desperation" that, in the worst-case scenario, may foreshadow a Chernobyl-like disaster.
Several experts, in a conference call with reporters, also predicted that regardless of the outcome of the atomic plant crisis, the accident will seriously damage the nuclear power renaissance.
The raging tsunami picked up shipping containers, cars and the debris of shattered homes. It crashed through the streets of Sendai and across open fields, forming a mud slick that covered vast tracts of land.
In Mimanisoma town, which was virtually obliterated by the tsunami's black tide of mud and debris, an AFP reporter saw fire volunteers collecting bodies they found in the twisted wreckage of what had once been a residential area.
Some 50,000 military and other rescue personnel are spearheading a mammoth rescue and recovery effort with hundreds of ships, aircraft and vehicles headed to the Pacific coast area.
The United States, which has nearly 50,000 military personnel in Japan, ordered a flotilla including two aircraft carriers and support ships to the region to provide aid.
The quake hit at 2:46 pm (0546 GMT) and lasted about two minutes, making buildings sway in greater Tokyo, the world's largest urban area and home to some 30 million people.
Two days after the first massive quake struck just under 400 kilometres northeast of Tokyo, aftershocks were still rattling the region, including a strong 6.8 magnitude tremor on Saturday and a 6.3 quake on Sunday.
Japan sits on the "Pacific Ring of Fire", and Tokyo is in one of its most dangerous areas, where three continental plates are slowly grinding against each other, building up enormous seismic pressure.
The government has long warned of the likelihood that a devastating magnitude eight quake would strike within the next 30 years in the Kanto plains, home to Tokyo's vast urban sprawl.
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