The 8.9-magnitude quake rocked buildings hundreds of miles to the south, sending petrified office workers into the streets in search of safety.
Transport services were crippled in large parts of northern Japan, while millions of homes suffered power outages. The self-defense forces said that between 60,000 and 70,000 people had been evacuated to 200 shelters in Sendai.
It is too early to gauge the true extent of the devastation but footage from the worst-hit regions suggest the death toll could climb dramatically in the coming days.
International agencies, meanwhile, have issued tsunami alerts across the region amid fears that the waves could engulf low-lying Pacific islands.
Several hours after the earthquake — the fifth strongest recorded anywhere in the world in the past century — police in Sendai said 200 to 300 bodies had been found after a neighborhood was overwhelmed by a wall of water.
A further 88 people have been confirmed dead and another 349 are missing.
The government declared a nuclear power emergency after reports that the cooling system at a nuclear facility in Fukushima prefecture, north of Tokyo, had malfunctioned. About 3,000 people living nearby have been evacuated, but officials in Tokyo said there was no immediate threat of a radiation leak. The International Atomic Energy Agency said all nuclear power plants in the affected area had shut down safely.
Flames could be seen leaping hundreds of feet into the air from an oil refinery in Chiba, northeast of the capital, while a major explosion was reported at a petrochemical complex in Miyagi prefecture.
Speaking to reporters after an emergency cabinet meeting, Prime Minister Naoto Kan said every effort would be made to “save the country,” and urged people to “stay calm.”
"The earthquake has caused major damage in broad areas in northern Japan," he said. ''Our government will make all-out efforts to secure people's safety and minimize the damage caused by the earthquake.”
Yukio Edano, the chief cabinet secretary, said: "Our initial assessment indicates that there has already been enormous damage. We will make maximum relief effort based on that assessment."
Thousands of Japanese self-defense force personnel are heading to the quake zone and Japan has accepted offers of help from U.S. military forces based in the country.
Rolling news coverage broadcast apocalyptic scenes of swaths of farmland in Sendai, nearly 200 miles north of Tokyo, being eaten up by a 30-foot-high tsunami. The wall of muddy water swept up homes, cars and even large boats in port as it continued its relentless journey inland.
Local media reports said the quake, which has been followed by as many as 50 strong aftershocks, has sparked at least 80 fires in cities and towns along a 1,300-mile-long stretch of coastline.
Tsunami warnings remain in place along Japan’s entire eastern coastline, while meteorological officials have said that the region can expect strong tremors in the coming hours and days.
An unknown number of people are missing after a train was reportedly engulfed by incoming waters, and a ship carrying 100 people has been swept out to sea.
In Tokyo, thousands of spooked office workers faced a night in evacuation shelters after the quake crippled subway and train services. Bullet trains to the north of Japan have been cancelled and air services remain sketchy across the country.
“There was a great rattling as things started to fall off the shelves in my office,” Chris Bunting, a British resident of Tokyo, told GlobalPost. “Some of the other staff were yelping. Others of a more practical frame of mind were trying to hold the moveable things down. I just stood rooted to the spot.
“After the room stopped rattling, everyone in my ninth floor office started trying to get in touch with their families and friends. The telephone and mobile networks were down, but the internet seemed to be working. I eventually managed to contact my pregnant wife, who is due in a couple of weeks, by email chat.”