Japan has lifted a tsunami advisory it issued for the north-eastern coast after a magnitude 6.9 earthquake, which seismologists said was an aftershock from the devastating March 2011 quake.

This morning small waves of 10 to 20 centimetres reached the coast off Iwate prefecture, 600 kilometres north of Tokyo, where Broadcaster NHK said thousands of residents had been ordered to evacuate.

"This quake is an aftershock of the 2011 quake that hit the Tohoku region," Japan Meteorological Agency (JMA) seismologist Yasuhiro Yoshida told reporters.

Towns along the north-eastern coast of Japan were levelled in a devastating tsunami in March 2011.

The agency warned residents against entering the ocean and said waves could continue to fluctuate for some time.

The US Geological Survey (USGS) said the earthquake had a magnitude of 6.8, while the JMA had earlier recorded it as 6.9.

The quake was measured at a depth of about 10 kilometres and struck just after 8:00am (local time). The epicentre was 210 kilometres east of the town of Miyako, the JMA said.

There were no immediate reports of injuries or casualties following the quake, local media said.

The city of Ofunato in Iwate issued an evacuation advisory to more than 1,350 households.

"We are using the emergency broadcast to advise people to keep away from the sea," Kozo Hirano, an Otsuchi Town official in Iwate, told Japan's public broadcaster NHK.

"The quake was pretty strong and lasted a long time so I thought there would be a tsunami warning."

The Pacific Tsunami Warning Centre in Hawaii said there was no danger of a Pacific-wide tsunami.

Large areas of the coastline covered by the advisory were damaged by the 2011 quake and tsunami that killed more than 18,000 people and triggered a nuclear accident in Fukushima.

Tohoku Electric Power Co (TEPCO), which operates the Onagawa and Higashidori nuclear plants in nearby Miyagi and Aomori prefectures, said it saw no irregularities at the facilities after the quake.

All 48 of Japan's nuclear reactors remain offline after the March 2011 earthquake and tsunami, which triggered the Fukushima nuclear disaster.

A spokesman for TEPCO, the operator of the Fukushima Daiichi and Fukushima Daini nuclear plants, said no irregularities were recorded. The quake was felt only weakly in the area, he said.

Unlisted Japan Nuclear Fuel also said there were no irregularities recorded at its nuclear fuel reprocessing facility or other plants in Aomori.

Earthquakes are common in Japan, one of the world's most seismically active areas.

Japan accounts for about 20 per cent of the world's earthquakes of magnitude 6 or greater.

ABC/wires