The first tremor off Hokkaido island was 6.8 magnitude and prompted some communities to issue evacuation orders or advisories to residents nearest the coast.
A swelling of 20 centimeters (8 inches) was observed in the port of Hachinohe in Aomori, northern Japan, about one hour after the quake struck the region. Smaller changes were also 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 centered just off the coast of Chiba, east of Tokyo, at a rather shallow 10 kilometers (6 miles) 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 Wednesday's first 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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