Tokyo inhabitants - set to enjoy a national holiday were woken shortly after dawn by the quake, which jolted the densely-built apartments and office blocks.
Local media said 17 people injured themselves as they stumbled while trying to take cover, with a 74-year-old Tokyo woman dislocating her shoulder.
Some objects fell from shelves and furniture wobbled, an AFP reporter saw.
The epicentre of the quake - which hit at 05:18 - was near Izu Oshima island southwest of central Tokyo, the Japanese meteorological agency said.
The US Geological Survey said the quake had a magnitude of 6.0, revised upwards from 5.8, and struck at a depth of 155 kilometres.
Nuclear damage avoided
It was the biggest tremblor felt in the Japanese capital since the 9.0-magnitude quake that hit northern Japan in March 2011, unleashing a killer tsunami and triggering the Fukushima nuclear crisis.
Japan Meteorological Agency said quakes of such depth do not usually cause many aftershocks, but warned the public that moderate aftershocks are possible for the next few days.
A number of train lines were automatically stopped as the quake struck, but were restarted again a short time later.
The Nuclear Regulation Authority said regional nuclear facilities avoided damage, including the crippled Fukushima Daiichi plant.
Three of the reactors at the plant went into meltdown after a huge 9.0-magnitude earthquake sparked a massive tsunami in March 2011.
The wave destroyed vast swathes of the coastline as it smashed into Japan's north-east, killing more than 18 000 people.
Japan is situated at the meeting place of several of the Earth's tectonic plates and experiences a number of relatively violent quakes every year.
But strict building codes frequently mean that even powerful quakes that might wreak havoc in other countries can pass without much damage.