The undersea quake struck at 5:57 local time at a depth of just 11.2 kilometres, 190 kilometres east of Morioka on Honshu island, it said.
On March 11, a massive magnitude 9.0 earthquake and subsequent tsunami devastated northeast region of the country, leaving more than 13,000 people dead and over 15,000 missing.
Since then, a number of strong aftershocks have hit the country.