An earthquake measuring 7.4 on the Richter Scale hit Fukushima in Japan on Tuesday, the weather agency said, leaving at least 12 people injured.
But the Japan Meteorological Agency downgraded the tsunami warning for northeastern prefectures of Miyagi and Fukushima to advisory, Xinhua news agency reported.
The epicentre of the quake was at a latitude of 37.3 degrees north and a longitude of 141.6 degrees east and occurred at a depth of 30 km.
The temblor was centred in the waters offshore of Fukushima, which borders the Pacific Ocean and is to the northeast of Tokyo.
Over 3,000 people fled to evacuation centres in Fukushima, the Japan Times reported.
"The sound of sirens brought back memories of the huge earthquake (of 2011)," said Tomomi Nagakubo, 48, who drove in her car to an evacuation centre in Ibaraki with her 13-year-old son.
At 8.03 a.m, 1.4-metre tsunami were observed at Sendai port in northeastern Miyagi prefecture, following the first wave of tsunami at coastline 20 km east of Iwaki city in Fukushima.
The weather agency warned of further tidal waves of up to three metres for Fukushima and one metre for other parts of the coastline facing the Pacific.
The jolt was felt in central Tokyo and also shook other northeastern Japanese prefectures including Tochigi and Ibaraki.
Train and flights services were partially suspended or delayed in northeastern Japan while power outage affected at least 1,100 households in Fukushima and Niigata.
Water supply was cut off at some parts in Fukushima and Sentai.
A nuclear fuel cooling facility of the Fukushima Daini nuclear power plant's No.3 reactor building stopped operating temporarily, while no abnormalities were observed at other nuclear plants in the country, according to power companies.
There have been no reports of significant damage from the quake or tsunami.