The quake had a preliminary magnitude of 7.3, the US Geological Survey said, and thousands of coastal residents were ordered to evacuate to higher ground, but the tsunami warning was lifted two hours after the tremor struck.
The March 2011 earthquake and following tsunami killed nearly 20,000 people and triggered the world's worst nuclear crisis in 25 years when the Fukushima-Daiichi nuclear plant was destroyed, leaking radiation into the sea and air.
Workers at the plant were ordered to move to safety after Friday's quake. Tokyo Electric Power Company, the operator of the Fukushima nuclear plant, reported no irregularities at its nuclear plants.
All but two of Japan's 50 nuclear reactors have been idled since the Fukushima disaster as the government reviews safety.
The quake measured a "lower 5" in Miyagi prefecture on Japan's scale of one to seven, meaning there might be some damage to roads and houses that are less quake resistant.
The scale measures the amount of shaking and in that sense gives a better idea of possible damage than the magnitude. The quake registered a 4 in Tokyo.
The one-metre tsunami hit at Ishinomaki, in Miyagi, at the centre of the devastation from the March 2011 disaster. All Miyagi trains halted operations and Sendai airport, which was flooded by the tsunami last year, closed its runway.
Five people in the prefecture were slightly injured.
"I was in the centre of the city the very moment the earthquake struck. I immediately jumped into the car and started running away towards the mountains. I'm still hiding inside the car," said Ishinomaki resident Chikako Iwai.
"...I have the radio on and they say the cars are still stuck in the traffic. I'm planning to stay here for the next couple of hours."
There are vast areas of Ishinomaki that still have not been cleaned up since last year's tsunami. Many houses lie in ruins, full of rubble. Workers by the shore still sort through thousands of cars that were swamped and destroyed. The cars are piled up and being taken apart for parts and scrap.
A quake every five minutes
Narita airport outside Tokyo was back in action after a brief closure for safety checks. There were small tsunamis, measuring in the centimetres, elsewhere near the epicentre.
Last year's quake, which measured 9.0, triggered fuel-rod meltdowns at Fukushima, causing radiation leakage, contamination of food and water and mass evacuations. Much of the area is still deserted.
The government declared in December that the disaster was under control.
"Citizens are now escaping to designated evacuation centres and moving to places on higher ground," office worker Naoki Ara said in Soma, 30 km (18 miles) from the Fukushima-Daiichi plant.
Prime Minister Yoshihiko Noda cancelled campaigning in Tokyo ahead of a December 16 election and was on his way back to his office, but there was no immediate plan to hold a special cabinet meeting.
Public spending on quake-proofing buildings is a big election issue.
Japanese were posting photos of their TV screens with tsunami warnings on Facebook, asking each other whether they're safe, confirming their whereabouts.
"It shook for a long time here in Tokyo, are you guys all right?" posted Eriko Hamada, enquiring about the safety of her friends.
Phone lines were overloaded and it was difficult to contact residents of Miyagi.
"Owing to the recent earthquake, phone lines are very busy, please try again later," the operator said.
The yen rose against the dollar and the euro on the news, triggering some safe-haven inflows into the Japanese currency.
Japan is one of the world's most earthquake-prone countries, with a tremor occurring at least every five minutes.
Located in the "Ring of Fire" arc of volcanoes and oceanic trenches partly encircling the Pacific Basin, the country accounts for about 20 percent of the world's earthquakes of magnitude 6.0 or greater.
Tokyo, with a population of 12 million, sits on the junction of four tectonic plates: the Eurasian, North American, Philippine and Pacific. The sudden bending or breaking of any plate can trigger an earthquake.