Cars, ships and buildings were swept away by a wall of water after the 8.9-magnitude quake, which struck about 400km (250 miles) north-east of Tokyo.
A state of emergency has been declared at a nuclear power plant but officials said there were no radiation leaks.
The death toll is unclear, but police say 200 to 300 bodies have been found in the port city of Sendai.
Many more people are unaccounted for.
With train services suspended, there are millions of people on the streets of Tokyo tonight. The official advice is, if you're safe, to stay where you are. But after the shock of the quake many people just want to get home.
Here in Tokyo, even though it wasn't the epicentre, the quake was still felt very powerfully. The ground rolled and rumbled underfoot and you could hear the great skyscrapers creaking and cracking as they swayed.
Walking was like crossing the deck of a ship at sea. People poured down from their offices and stood in the street staring up.
The tremor, measured at 8.9 by the US Geological Survey, hit at 1446 local time (0546 GMT) at a depth of about 24km.
A tsunami warning was extended across the Pacific to North and South America.
The Red Cross in Geneva warned that the waves could be higher than some Pacific islands, Reuters news agency said.
Coastal areas in the Philippines, and other parts of the Pacific were evacuated ahead of the tsunami's expected arrival.
The first waves, currently under a metre high, have started reaching Hawaii.
New Zealand downgraded its alert to a marine threat, meaning strong and unusual currents were expected.
'Train missing'
Strong waves hit Japan's Miyagi and Fukushima prefectures, officials said, damaging dozens of coastal communities.
Kyodo news agency said a 10-metre wave (33ft) struck Sendai, which is in Miyagi.
Japan's NHK television showed a massive surge of debris-filled water sweeping away buildings, cars and ships and reaching far inland.
Motorists could be seen trying to speed away from the wall of water.
A passenger train with an unknown number of people aboard was missing in one coastal area, police told Kyodo.
And a ship carrying 100 people was swept away, Japanese media reported, quoting police in Miyagi. It is not clear what happened to the vessel.
Farmland around Sendai was submerged and the waves pushed cars across the runway of the city's airport. Fires broke out in the city's centre.
Thousands of people are being evacuated from near the Fukushima power plant, where a state of emergency has been declared. The cooling system failed in one of its reactors when it shut down automatically because of the earthquake.
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Prime Minister Naoto Kan said no radiation leaks at that power plant or any of the other reactors in the quake-hit zone had been detected.
The UN's nuclear agency said four nuclear power plants had shut down safely.
In Iwate prefecture, also near the epicentre, an official said it was difficult to gauge the extent of the destruction.
"Roads were badly damaged and cut off as the tsunami washed away debris, cars and many other things," said Hiroshi Sato, a disaster management official in Iwate.
The earthquake also triggered a massive blaze at an oil refinery in Ichihara city in Chiba prefecture near Tokyo, engulfing storage tanks.
There were reports of about 20 people injured in Tokyo after the roof of a hall collapsed on to a graduation ceremony.
Residents and workers in Tokyo rushed out of apartment buildings and office blocks and gathered in parks and open spaces as aftershocks continued to hit.
Many people in Tokyo said they had never felt such a powerful earthquake.
In central Tokyo, Jeffrey Balanag said he was stuck in his office in the Shiodome Sumitomo building because the elevators had stopped working.
"We're almost seasick from the constant rolling of the building," he told the BBC.
Bullet train services to northern Japan were halted and rapid transit in Tokyo was suspended, stranding many workers in the city centre.
About four million homes in and around Tokyo suffered power outages.
In a televised address, Mr Kan extended his sympathy to the victims of the disaster and said an emergency response headquarters had been set up.
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