The quake hit at 8:44pm local time (1144 GMT) at a depth of 63 kilometres (39 miles), in the Chiba prefecture which neighbours Tokyo.
Service on a high-speed train line was briefly halted but later resumed after a track inspection.
Neither the Tokyo-Narita airport nor any nuclear installations in the region were affected, public broadcaster NHK said.
The tremor came exactly one week after another 5.5 struck close to the capital, and three weeks after a major 7.1 magnitude quake generated small tsunamis on Japan's north-east coast, without causing damage or casualties.
More than 18,000 people died when a 9.0-magnitude sub-sea earthquake sent a towering tsunami barrelling into Japan's northeast coast in March 2011 in the country's worst post-World War II disaster.
Cooling systems at the Fukushima nuclear plant were knocked out, sending reactors into meltdown and forcing tens of thousands of people to flee.