The agency said a 1.2 metre (about four feet) tsunami reached the remote southern island of Amami Oshima around 11:55pm (1455 GMT) Saturday before other areas along Japan's Pacific coast observed smaller tsunami.
The eastern shores of northernmost Hokkaido island as well as southwestern regions of Kochi and Wakayama also saw tsunami as high as 0.9 metres shortly after midnight, the agency said.
National broadcaster NHK switched to special programming and aired live footage from ports of affected regions, calling on area residents to evacuate to higher ground.
The footage showed no clear signs of abnormality, however.
A weather agency official told a televised, midnight news conference that the agency had detected a tidal change higher than one metre after 11pm.
The agency didn't immediately classify it as tsunami. However, it decided to activate the public tsunami warning systems to urge the evacuation of Amami residents.
"We don't know at this point whether this is tsunami, but a strong tidal change has been observed, so we're urging residents to respond," the official told the press conference.
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