The port town of Ofunato, Iwate prefecture, saw a 10-centimetre (four-inch) tsunami at 10:44 am (0144 GMT), the agency said.
The agency issued a tsunami advisory for Iwate, Miyagi, and Fukushima prefectures after a 7.1-magnitude earthquake struck off the main island of Honshu at 09:57 am (0057 GMT). No damage has been reported from the tsunami and quake.
Television footage of the port in Ofunato did not show any visible sign of the tsunami, with the water surface seemingly calm and flat.
The agency issued the tsunami advisory shortly after the offshore quake in the same general area as the 9.0-magnitude quake of March 11 which triggered a massive tsunami.
The US Geological Agency, which also estimated the magnitude at 7.1, said the offshore quake hit at a depth of 10 kilometres (6.2 miles).
Tokyo Electric Power Co (TEPCO) said it had not received reports of any fresh problems at the crippled Fukushima Daiichi nuclear plant after the latest earthquake. "We are still checking details, but cooling of reactors is continuing," a TEPCO spokeswoman said.
But the company told work crews near the water to seek higher ground due to the tsunami advisory.
The Japanese weather agency expected a small tsunami of up to 50 centimetres (20 inches) along the affected region. Communities along the Pacific coast issued warnings and advisories for local residents to seek higher ground but no damage had been reported shortly after the quake. (AFP)
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