The quake has sparked fires in several areas including Tokyo, and numerous casualties are feared.
The tremor hit at 1446 local time (0546 GMT). Seismologists say it is one of the largest earthquakes to hit Japan for many years.
The tsunami warning was extended to the Philippines, Indonesia, Taiwan, the Pacific coast of Russia and Hawaii.
The Pacific Tsunami Warning Center said the wave could extend as far as Chile.
Tsunami waves hit Japan's Miyagi and Fukushima prefectures, officials said.
Japan's NHK television showed a massive surge of debris-filled water sweeping away buildings, cars and ships and reaching far inland.
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.
Bullet train services to northern Japan were halted, rapid transit in Tokyo was suspended and some nuclear power plants automatically shut down.
Prime Minister Naoto Kan said there had been no radiation leaks.
In a televised address, he extended his sympathy to the victims of the disaster and said an emergency response headquarters had been set up.
He said the earthquake had a magnitude of 8.4 while the US Geological Survey said it measured 8.9.
latest message from Google: Tsunami Alert for New Zealand, the Philippines, Indonesia, Papua New Guinea, Hawaii, and others. Waves expected over the next few hours, caused by 8.9 earthquake in Japan.