The initial quake measuring 8.0 on the Richter scale occured near the port of Erimo, about 975km north of Tokyo.
A second tremor measuring 5.8 on the Richter scale jolted Hokkaido about an hour later, followed by another registering 7.0, the meteorological agency said.
Authorities issued a tidal wave warning on television soon after. A local television showed video of a fire at an oil refinery after the quake.
The tremors were said to be strong enough to damage houses, trigger landslides and crack up roads.
The meteorological agency issued a tsunami warning for the coastal areas in eastern and central Hokkaido and a tsunami alert for the coastal areas in western Hokkaido as well as the northern Japanese prefectures of Aomori, Iwate, Miyagi and Fukushima.
The massive quake caused a fire
Major highways were closed and rail services halted in many areas. The tremors also caused major power blackouts.
Kiichi Inque, cabinet minister in charge of disasters said helicopters had been sent to the area to assess the damage.
Hokkaido, about the size of Austria, is the second largest of Japan’s four main islands and home to a nuclear reactor and active volcanoes.
Sitting atop the junction of at least three tectonic plates, whose gradual movements trigger earthquakes, Japan is one of the world’s most quake-prone areas.
About 500 people were injured and a similar number of homes damaged or destroyed in an earthquake in July in Miyagi, 300km north of Tokyo.
Far worse was the quake that hit the city of Kobe eight years ago, killing more than 6000 people.