The Japanese Meteorological Agency said the tsunami, generated by a magnitude eight tremor, could reach Russia's Kuril Islands, but Russian services said the threat was not imminent.
The wave was estimated to be no higher than 40 centimeters (16 inches) when it hit Honshu, but it rose to almost 2 meters (6.5 feet) as it came ashore at the port of Nemuro, on Hokkaido's east coast, at 9:29 p.m. (12.29 GMT).
In a tsunami warning, Japan's meteorological agency urged residents of Hokkaido and Honshu to flee coastal areas and move to higher ground for safety. A warning was also issued for Russia's Kuril Islands.
The Russian Emergency Situations Ministry said the earthquake measured 8.1 to 8.5 on the Richter scale.
A local emergencies ministry official said Severo-Kurilsk, in the North Kurils, was hit by an earthquake measuring three on the Richter scale.
Russian rescuers started evacuating people in the South Kurils in response to the warning, but the threatened tsunami skirted the islands and people are now returning to their homes, the ministry said.
