At least six people were killed, 20 injured and many were missing, including a number of children who were sucked into the sea, the public broadcaster NHK reported.
The six deaths were reported at a welfare facility that collapsed in Minami Soma in Fukushima prefecture, and the Kyodo News agency said eight people were missing in a landslide in Fukushima prefecture.
Waves swamped buildings and swept away cars, boats, crops and even buildings. People gathered on the roofs of inundated buildings and houses. Women waved white handkerchiefs from windows, seeking help.
NHK showed footage of submerged vehicles in Kamaishi, Iwate prefecture, as the tsunami hit the city's coast and of many houses in Sendai, Miyagi prefecture, being washed away by quake-generated waves.
High tsunami waves also hit Hiroo on Hokkaido, Japan's northern island.
The agency warned more waves up to 13 feet high would hit the coast of eastern Japan.
A tsunami advisory was issued in wide swathes of the eastern coast and around the Pacific.
The quake was earlier reported at magnitude 7.9 by Japan's Meteorological Agency. The U.S. Geological Survey upgraded it to 8.9 on the Richter scale.
The quake, which hit at 2:46 p.m. shook buildings in Tokyo violently and some caught fire.
The U.S. Geological Survey said the initial quake was followed by at least eight large aftershocks, the strongest measuring magnitude 7.1 and striking 40 minutes after the first tremor.
Media reported extensive damage to buildings in and around Tokyo and the collapse of roofs on Tokyo buildings.
NHK showed footage of fire at petrochemical complexes in Ichihara, Chiba Prefecture, east of Tokyo.
Narita International Airport and airports in Senda, Iwate Hanamaki, Aomori and Yamagata were closed, the Jiji Press agency said. NHK showed footage of the Sendai Airport submerged.
Nuclear power stations on the Pacific coast in Miyagi and Fukushima prefectures shut down operations automatically after the quake hit.
More than 4.5 million households experienced power outages in the metropolitan area, Tokyo Electric Power Co said. Almost all the households in eastern Japan experienced power failures, NHK said.
Japanese train service, including bullet trains, were suspended in northeastern and central Japan.
The Pacific Tsunami Warning Center in Hawaii issued tsunami warnings for Japan, Russia, Marcus Island and the Northern Marianas and tsunami watches for Taiwan, the Philippines, Indonesia, Hawaii, Guam and other Pacific islands.