The port towns of Soma and Ofunato saw 10-centimetre (four-inch) tsunami waves triggered by the 7.3-magnitude earthquake that struck off the main island of Honshu at 9:57 am (0057 GMT), the agency said.
No damage has been reported from the tsunami and quake, which was strong enough to sway skyscrapers in Tokyo, some 400 kilometres from the epicentre.
The Japanese agency and the US Geological Survey originally estimated the quake's magnitude at 7.1, hitting the same general area as the 9.0-magnitude quake of March 11 which triggered a massive tsunami.
While Japan upgraded the quake to 7.3, the US agency revised it down to 7.0, centred 212 kilometres (131 miles) east of Sendai city, Miyagi prefecture, at a depth of 34.9 kilometres.
The Japanese agency lifted the tsunami advisory at 11:45 am.
"Changes in sea level may occur for the next few hours. Please use caution when conducting activities near the ocean, such as swimming and surf fishing," a Japanese weather agency official told a news briefing.
Television footage of Ofunato and Soma did not show any visible sign of the tsunami, with the water surface seemingly calm and flat.
Tokyo Electric Power Co (TEPCO) said the latest quake did not cause fresh problems at the crippled Fukushima Daiichi (number one) nuclear plant and the nearby Fukushima Daini (number two) plant.
"We have received reports that there has been no significant impact at the Fukushima Daiichi and the Fukushima Daini nuclear plants," a TEPCO spokesman told a news conference.
Cooling of crippled reactors at Fukushima Daiichi continued, although the company told work crews near the water to seek higher ground during the tsunami advisory.
The Japanese weather agency originally 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 or to leave areas near the water.
"For a second, I thought maybe another big one will come," a middle-aged man in coastal Kesennuma, Miyagi, told national broadcaster NHK.
The devastating March 11 and tsunami left about 22,000 people dead or missing and triggered an atomic crisis at the Fukushima Daiichi nuclear plant.