A small tsunami hit Japan's northeastern coastline on Wednesday, officials said, after a strong earthquake rocked the region almost exactly a year on from the country's worst post-war natural disaster.

A 6.9-magnitude quake struck 26.6 kilometres (16 miles) below the seabed off the northern island of Hokkaido in the Pacific at 6:08 pm local time (0908 GMT), the US Geological Survey said.

It was followed by a 20 centimetre (eight inch) tsunami which had prompted local authorities to issue an evacuation warning for coastal residents before it hit land.

The waves hit several locations in Hokkaido as well as Aomori prefecture, which was one of the areas in Japan's northeast devastated by last year's disaster.

The Japanese meteorological agency had initially said a tsunami could be as high as 50 centimetres, but US monitors said there was no Pacific-wide tsunami threat.

The initial quake was followed by several powerful aftershocks in the same vicinity, including one with a magnitude of 6.1, but there was no tsunami warning.

Almost three hours after the first quake, a 5.7-magnitude shock struck 90 kilometres east of Tokyo, USGS said. Japanese officials said there was no fear of a tsunami "although sea levels may change slightly in a few hours".

The quakes come after a 9.0-magnitude earthquake triggered a monster wave on March 11 last year that killed more than 19,000 people and crippled Japan's Fukushima nuclear plant.

The tsunami swamped cooling systems at the Fukushima site and sent three reactors into meltdown, spewing radiation into the environment and sparking the world's worst atomic accident in a generation.

There were no immediate reports of damage at nuclear facilities in the area affected by Wednesday's quake.

A spokesman for Tohoku Electric Power, which operates two nuclear power plants in the country's northeast, said the facilities were unaffected.

"We have not monitored any change in radiation levels around the facilities following the quake," he told AFP.

The meteorological agency had also warned the tsunami could reach the Kuril islands, off Hokkaido, which Russia has controlled since Japan's surrender at the end of World War II.

On Sunday, Japan fell silent to remember last year's tragedy, with tearful families gathering in towns and villages across the country's shattered northeast to remember those they lost when the towering waves smashed ashore.

Tens of thousands were forced to evacuate a 20-kilometre exclusion zone immediately around the Fukushima plant, while many families with small children moved away from the prefecture completely.

Sunday's anniversary also saw thousands protest against nuclear power in demonstrations across the world.

Japan has temporarily shut most of its 54 commercial nuclear reactors, but plans to re-open the plants has set off a highly-charged debate in a country prone to earthquakes.

On Monday, a group of Japanese citizens filed a lawsuit to prevent the restart of a nuclear power plant, warning that there was little proof the reactors would were quake-resistant.

The disaster also hammered Japan's already struggling economy, stoked fears about radioactive contamination in the food chain and set off multi-billion dollar reconstruction efforts.