The 5.4-magnitude quake, with its epicentre located in Tokyo Bay, struck at 5:49 AM local time, according to the US Geological Survey.
The Japan Meteorological Agency said no tsunami warning had been issued, and that the quake was 70 kilometres deep.
Residents said the quake was not strong enough to knock things from shelves. It prompted a handful of reports of possible injuries, including a woman who complained about being hurt after falling from her bed, according to national broadcaster NHK.
The tremor did not cause any damage to the region's nuclear facilities, according to the government, and did not affect the areas that host the crippled Fukushima Daiichi nuclear plant, which went through meltdowns after a 9.0-magnitude quake and tsunami disaster in 2011.
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It served as a reminder that a huge earthquake could strike the Japanese capital - which has a population of about 13 million people - at any time.
Experts have long warned Japan to stay vigilant for the next "Big One", and a powerful 7.8-magnitude earthquake struck off the coast in May.