A replica with a powerful magnitude, of 6.7 took Friday offshore 373 km (231 miles) away from Tokyo region, the Japanese Meteorological Agency said.
Also a tsunami alert was issued Friday for almost all coasts of the Pacific, including Australia and South America.
Local media reported at least 50 deaths, with more casualties feared. According to images broadcast on television, the balance would grow, and the Defense Ministry dispatched ships to participate in rescue operations.
Authorities have warned against waves that could reach up to six meters high, and public television NHK announced a 4.2 meter high tsunami in Port Kamaishi, Iwate Prefecture (northeastern).
The 8.9-magnitude quake, according to the American Geological Institute USGS, occurred at 24.4 km depth, at 2:46 p.m. about 100 kilometers offshore Miyagi prefecture.
“I wasn’t scared when it started … but it just kept going and going,” said Michelle Roberts, who lives in central Tokyo. “I won’t lie, it was quite scary. But we are all OK. We live on the third floor, so most everything shook and shifted.”
A spokesman for the U.S. military bases in Japan said all service members were accounted for and there were no reports of damage to installations or ships.
President Barack Obama, while offering his condolences, said the United States was standing by to help “in this time of great trial.”
Japanese Prime Minister Naoto Kan said an emergency task force has been activated, and appealed for calm. He said there were no reported leaks of radioactive materials from power plants.
“This was larger than anyone expected and went on longer than anyone expected,” said Matt Alt, who lives in Tokyo.
“My wife was the calm one … she told us to get down and put your back on something, and leave the windows and doors open in case a building shifts so you don’t get trapped.”
Another tsunami alert was issued for Japan, Russia, Mariana Islands, Philippines, Guam Island, Taiwan, Marshall Islands, Indonesia, Papua New Guinea, Nauru, Micronesia and Hawaii.