Two hours after the tremor, which struck at 4.52pm (0752 GMT) on Monday, tsunami waves as high as 80cm had been detected, though warnings remained for possible bigger waves at the top of Japan's main Honshu island, and the northern Hokkaido region.
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.
Big aftershocks could occur in the following days and weeks, an official from Japan's Meteorological Agency (JMA) said at a separate televised press conference.
Prime Minister Sanae Takaichi said earlier the government had set up an emergency task force and urged citizens in the affected areas to evacuate.
"Possible damage and casualties are now being looked into," Takaichi told reporters at her offices in Tokyo.
Ships sailed out of Hachinohe port in Hokkaido in anticipation of the waves, footage aired on NHK showed, as a "Tsunami! Evacuate!" alert flashed across the screen.
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 10km deep, JMA 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.
