But the meteorological agency lifted the warning about an hour after the latest jolt hit at 6.51am (7.51am AEST) about 50km off the east coast of Miyako, Iwate prefecture, at a depth of 20km in the Pacific.
The northeast coast of Japan's main Honshu island was ravaged by a 9.0 magnitude quake and monster tsunami on March 11, which left more 23,000 people dead or missing.
The disasters also crippled the Fukushima Daiichi nuclear power plant, triggering the world's worst atomic accident since Chernobyl in 1986 and forcing hundreds of thousands of residents to leave their homes.
Japan's Kyodo news agency reported that the meteorological agency issued a tsunami warning for Iwate Prefecture.
The US Pacific Tsunami Warning Center said that it did not expect a destructive Pacific-wide tsunami.
There were no immediate reports of damage or injuries.
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