The earthquake registered a major 8.1 on the Richter scale some 600 kilometres (370 miles) north-east of Japan's main northern island of Hokkaido, according to the Japan Meteorological Agency.
The area where the quake hit is isolated, with the Russian-administered Kuril island chain the closest populated area.
Japan issued warnings for all of its east coast from Tokyo on north, saying that seismic waves of up to two meters (six and a half feet) could strike the shore.
But the first tsunami known to hit the coast was a mere 40 centimetres (15.75 inches). It struck the north-eastern Japanese town of Nemuro at 9:42 p.m. (1242 GMT), 87 minutes after the earthquake.
However, Japanese officials warned that the threat was not over. In Tokyo, the government set up a special communication office to collect information about the tsunami.
"The tsunami warnings and advisories are still out there and the first tsunami waves are beginning to be observed. People need to remain cautious," Takeshi Hachimine, a meteorological agency official, told a news conference.
The US Pacific Tsunami Warning Center said the warning was in effect for both Russia and Japan along with the Pacific islands of Marcus, Wake and Midway.
It issued a tsunami watch for areas including Indonesia -- which is still recovering from the devastating December 2004 earthquake -- along with Hawaii, the Philippines and Taiwan.
"An earthquake of this size has the potential to generate a destructive tsunami that can strike coastlines in the region near the epicentre within minutes to hours," it said.
The West CoastAlaska Tsunami Warning Center in Palmer, Alaska issued a tsunami warning covering the areas from Sand Point, Alaska to Attu, Alaska.
It said a tsunami watch was in effect for Washington state and British Columbia, as well as the area from Cape Flattery, Washington to Sand Point, Alaska.
"At this time, this message is advisory only for other areas of California, Oregon and Washington," it added.
Japanese officials urged residents to head to higher ground, a warning passed on by local authorities. Hokkaido authorities said they were issuing mandatory evacuation orders for 10 municipalities.
The quake was too far away to be felt in Japan's major population centres.
Television footage showed rain but relatively calm waters on Nemuro, a Japanese port city facing the Kuril chain which witnessed the first tsunami.
"We have issued an evacuation warning to all residents living near the coast," said Hiroyuki Taniguchi, a local official in Nemuro. "We have not had any sign of high waves. So far, there is no confusion in the city. We did not feel any jolts," he said.

Copyright AFP (Agence France-Presse), 2006