An earthquake measuring 7.3 on the Richter scale Friday jolted the east coast of Honshu island, leading to a tsunami warning for the coastal areas which was later lifted in Miyagi prefecture, Xinhua reported.
The quake, which occurred at 5.18 p.m., had a depth of 10 km, the Japan Meteorological Agency (JMA) said. Earlier, the the US Geological Survey (USGS) had put the origin at a depth of 36 km.
At least five people were injured in Miyagi after the quake.
The tremor shook buildings as far away as Tokyo. The temblor was followed by a 6.2-magnitude aftershock off the east coast of Honshu, at 08.31 GMT, the USGS said.
Japan's Nuclear Regulation Authority said no abnormalities had been detected at nuclear plants in the northeast, including the Fukushima Daiichi nuclear plant which was badly damaged in March 2011 earthquake and following tsunami.
Sendai airport in Miyagi grounded all flights while Narita airport near Tokyo briefly closed its runways.
Japanese Prime Minister Yoshihiko Noda cancelled his campaign speech in Tokyo and returned to his office to deal with the emergency.
The tsunami warning for Japan's northeastern coastal areas was lifted, media reported here in the evening.
The warnings for the northeastern Miyagi prefecture were lifted at 7.20 p.m. by Japan Meteorological Agency (JMA), reported Japanese broadcaster NHK.
Earlier, one-metre tsunami had reached Ishinomaki, Miyagi prefecture, the centre of the devastation during the March 2011 disaster, at 6.02 p.m.
According to JMA, as the earthquake jolted the east coast of Honshu, it led to a tsunami warning for the country's northeastern coastal areas.
Nearly 16,000 people had been killed in a 7.2 Richter earthquake and a subsequent tsunami that struck Japan March 11 last year.
The Miyagi prefecture had registered the greatest damage in its vicinity.