Meteorologists said the wave swept ashore at just after 6 pm (0900 GMT) in Ishinomaki, a city badly hit by the 2011 tsunami that wrecked a large swathe of the northeast coast, killing thousands.
There were no immediate reports of any fatalities after the 7.3-magnitude quake that was followed by a 6.2 aftershock, according to the United States Geological Survey.
Residents of at least one town, Minamisanriku in Miyagi prefecture, were advised to get to safety, with reports suggesting other towns were also affected.
"We are now calling on people to evacuate to higher ground," town official Ryuichi Omori said. "It's already pitch dark here. Calls phones – both landlines and mobiles – are not going through now, which makes it difficult to see people's movement.
"The quake was not so big although it felt very (strong). It was not big at all compared with last year's earthquake. The town office is now setting up a disaster taskforce."
A presenter on state broadcaster NHK repeatedly told viewers to get to safety after the initial tremors, which set Tokyo buildings swaying violently.
NHK, quoting the national meteorological agency, said the tsunami was expected to hit the coast of Iwate at 5:40 pm (08:40 GMT), Fukushima at 5:50 pm, and Aomori and Ibaraki at 6:00 pm.
The 7.3 quake struck 23 miles under the Pacific, USGS said. The epicenter was 176 miles east of Sendai, or 285 miles northeast of Tokyo, according to the USGS.
NHK said the Japan Meteorological Agency had issued a tsunami warning, one notch lower than a tsunami alert, for the Pacific coast of Iwate, Fukushima, Aomori and Ibaraki prefectures.
There was no threat of a Pacific-wide tsunami, US monitors based in Hawaii said. Officials in both Indonesia and the Philippines south of Japan said there was no threat of a localized tsunami.
Nuclear plant operator Tokyo Electric Power told AFP there were no reports of any problems at the crippled Fukushima nuclear plant.
"No abnormalities have been recorded on instruments at Fukushima Daiichi nuclear plant's six reactors," a TEPCO spokesman said.
"All workers were ordered to take shelter inside buildings at the Fukushima plant.
"No abnormalities were confirmed with the radiation monitoring posts at the Fukushima plant. No abnormalities were seen with the water processing facilities."
Prime Minister Yoshihiko Noda was heading to his office where he would be monitoring the situation, Jiji Press said.
Japan Railways East temporarily suspended Shinkansen bullet train services to check any damage, Jiji said, while Haneda Airport near central Tokyo was reported to be operating normally.
Narita airport was reported to have resumed operations after a temporary suspension.