The massive wave of water, as high as 10 metres in some parts, reached more than five kilometres inland.
The meteorological agency issued its top-level evacuation alerts for the entire Japanese coast amid warnings of a tsunami of between six and 10 metres.
Towns and farms around Sendai city in northern Japan have been engulfed by a seven-metre tsunami, while a four-metre wave swamped parts of Kamaishi on the Pacific coast.
Residents have been ordered to high ground and stay away from the coast as tsunamis can strike in several waves.
Seismologists say the quake was 160 times more powerful than the one that devastated Christchurch last month.