The death toll how now reached at least 29 people, police and authorities have said, while some news agencies are putting it as high as 32.
According to the AFP news agency the dead include a 67-year-old man crushed by a wall and an elderly woman killed by a fallen roof in greater Tokyo.
It quotes the National Police Agency as saying "the damage is so enormous that it will take us much time to gather data".
Meanwhile a fire has also broken out in the turbine building of a nuclear plant in the Miyagi prefecture, local news agencies said. A fire broke out in the turbine building of
Onagawa nuclear plant in Miyagi Prefecture on Friday, Kyodo News reported, raising concerns of a radioactive leak.
Earlier Naoto Kan, the prime minister, said no radiation leaks had been reported from any of Japan's nuclear power stations, and four plants closest to the quake had been safely shut down.
A number of amateur videos from Japan are surfacing on YouTube, showing chaos unfolding as the earthquake struck, including this one said to be taken in Tokyo:
A tsunami is expected to hit Indonesia within the hour, authorities say.
Step Vaessen, Al Jazeera's correspondent in Jakarta, said: "Lots of people are going away from the beaches because they are hearing from other sources, not from the authorities, that a tsunami might hit."
But the country is only expecting small waves to hit, she said. "It's a very different picture than what we're hearing from the Philippines."
The death toll from the earthquake has now reached 17, according to the Japanese government.
The disaster triggered fires in the north-east of the country, including at gas storage tanks at the Cosmo oil refinery in Ichihara city, Chiba Prefecture, near the capital Tokyo.