People were being warned to stay away from the coast with the small wave rolling ashore in Ishinomaki around an hour after the 7.1 magnitude quake.
Workers at the crippled Fukushima nuclear plant were "ordered to evacuate from the waterfront", Kyodo reported, also quoting the Tokyo Electric Power Company (TEPCO) as saying no new abnormalities had been found at the power station.
The quake struck at a depth of 10 kilometres at 2:10am local time (1710 GMT Friday), 327 kilometres southeast of Ishinomaki in Miyagi Prefecture, according to the US Geological Survey.
In the town of Ofunato, a 20-centimetre tsunami was logged just after 3 am. The waves were expected to hit several places along the northeast coast that was devastated by the huge tsunami of 2011.
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NHK was telling viewers in the area that there remained a possibility that secondary waves could strike, but live footage from harbours in several towns showed no significant changes.
Eastern Japan, a seismically active region, was struck by a 6.5 magnitude earthquake last month causing tremors that were felt 600 kilometres away in Tokyo.
Cooling systems at the Fukushima nuclear plant were knocked out, sending reactors into meltdown and forcing tens of thousands of people to flee.