A strong earthquake measuring 6.6 on the Richter scale shook northern Japan on Saturday, triggering a minor tsunami, the meteorological agency said.
There were no immediate reports of casualties or damage.
The tremor struck at 11:39 am (0239 GMT) with its epicentre located in the Pacific off Fukushima prefecture at a depth of 10 kilometres (6.2 miles), the agency said.
A 20-centimetre-high (eight-inch) tsunami was observed in Miyagi and other areas north of Tokyo after the agency warned tsunami tidal waves up to 50 centimetres would hit coastal areas in the region.
An aftershock measuring 5.3 on the Richter scale hit northern Japan shortly after the first jolt, the agency said.
The government set up a liaison office at the crisis management centre at the prime minister's office in Tokyo.
A powerful quake hit the northern prefecture of Miyagi on June 13, killing 13 people with another 10 missing.
Japan experiences 20 percent of the world's major earthquakes.