Authorities warned that the northeastern coastline could see towering waves after the quake struck off the coast of Hokkaido.
Hazardous waves were possible up to 620 miles from the epicentre, threatening Japan and Russia, the Pacific Tsunami Warning Center (PTWC) said.
A wider advisory was issued for smaller waves of up to a metre along the eastern coastline.
Several people were injured at a hotel in the Aomori town of Hachinohe, local media 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.
Residents in the areas under tsunami warnings have been told to evacuate as quickly as possible.
Authorities warn that waves can strike repeatedly, and tell residents to keep away until the notice is over.
Those in areas under advisory are told to keep away from coasts and rivers vulnerable to overflowing.
Nuclear power plants in the region are also conducting safety checks following the tsunami warning, public broadcaster NHK reported.
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" of volcanoes and oceanic trenches partly encircling the Pacific Basin, Japan accounts for about 20pc of the world's earthquakes of magnitude 6.0 or greater.