The agency said the magnitude 7.6 quake struck off the coast of Hokkaido, near the coastal city of Aomori, with an epicentre about 50 kilometres below the sea surface.
It issued an alert in the region for a tsunami of up to three metres.
The warnings were issued for the prefectures of Hokkaido, Aomori and Iwate, and a tsunami of 40cm had been observed at Aomori's Mutsu Ogawara and Hokkaido's Urakawa ports, the agency said.
Nuclear power plants in the region were conducting safety checks, public broadcaster NHK reported.
Several people were injured at a hotel in the Aomori town of Hachinohe, NHK reported.
Prime Minister Sanae Takaichi said the government set up an emergency task force to urgently assess the extent of damage.
"We are putting people's lives first and doing everything we can," she said.
Japan is one of the world's most earthquake-prone countries, with a tremor occurring at least every five minutes.
East Japan Railway suspended some train services in the area, which was also hit by the massive 9.0-magnitude quake in March 2011.
Located in the Ring of Fire arc of volcanoes and oceanic trenches partly encircling the Pacific Basin, the country accounts for about 20 per cent of the world's earthquakes of magnitude 6.0 or greater.
with Reuters
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