Two hours after the tremor, which struck at 4.52pm (0752 GMT) on Monday, tsunami waves as high as 80cm had been detected.
A tsunami warning was later downgraded to a tsunami advisory.
There were no immediate reports of casualties or major damage, Japan's top government spokesman Minoru Kihara told a news conference as night fell in the capital Tokyo.
Several port towns including Otsuchi and Kamaishi - both hard-hit by a massive earthquake and tsunami in 2011 - earlier issued evacuation orders for thousands of residents, according to public broadcaster NHK.
Bullet train services were halted and some motorways were closed due to the tremors.
Following the quake, the government issued a warning of a heightened risk of a megaquake.
Normally, the probability of an earthquake of magnitude 8.0 or stronger striking along the Japan Trench and Kuril Trench in the Pacific off northern Japan in a week is about 0.1 per cent, but during the week that follows Monday's quake, it will be higher at about 1.0 per cent, a government official told reporters.
"Please take anti-disaster steps, while embracing the idea that one must protect one's own life," the official said.
The quake measured an "upper five" on Japan's seismic intensity scale - strong enough to make it difficult for people to move around and cause unreinforced concrete-block walls to collapse.
The tremor had an epicentre in the Pacific Ocean and was 20km deep, the Japan Meteorological Agency said.
A three-metre tsunami could cause damage to low-lying areas, flooding buildings, and anybody exposed would be caught in its currents, according to JMA
Located in the "Ring of Fire" of volcanoes and oceanic trenches partly encircling the Pacific Basin, Japan is one of the world's most earthquake-prone countries, with a tremor occurring at least every five minutes.
It accounts for about 20 per cent of the world's earthquakes of magnitude 6.0 or more, such as the 2011 disaster that caused nuclear meltdowns at a Fukushima power plant.
There are no nuclear power plants currently in operation in the affected areas and Hokkaido Electric Power Co and Tohoku Electric Power Co said there were no abnormalities reported at their idled facilities there.
