The strongest tremor, off Hokkaido island, was 6.8 magnitude and caused tidal changes that prompted some communities to issue evacuation orders or tsunami advisories to residents nearest the coast.
A swelling of 20 centimetres was observed in the port of Hachinohe in Aomori, northern Japan, about one hour later. Smaller changes were reported in several locations on Hokkaido island and Aomori prefecture.
The Japan Meteorological Agency lifted all tsunami advisories about an hour and half later.
The earthquake felt in Tokyo was magnitude 6.1 and centred just off the coast of Chiba, east of Tokyo, at a rather shallow 10 kilometres below the sea surface.
The town of Otsuchi in Iwate prefecture, where more than 800 died in last year's tsunami, issued an evacuation order to coastal households as a precaution after the 6.8 quake, said prefectural disaster management official Shinichi Motoyama. No damage or injury was reported, he said.
Iwate was heavily damaged by last year's earthquake and tsunami. Thousands of aftershocks have shaken the region since then, nearly all of them of minor or moderate strength.
The magnitude 9.0 earthquake and tsunami on March 11, 2011 left some 19,000 people dead or missing.
Japan marked the first anniversary of the disasters on Sunday, as the country still struggles to rebuild.
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