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. Some objects fell from shelves and furniture wobbled, an AFP reporter saw.
The epicentre of the quake – which hit at 5:18 am (2018 GMT Sunday) – was near Izu Oshima island southwest of central Tokyo, the Japanese meteorological agency said. The US Geological Survey (USGS) said the quake had a magnitude of 6.0, revised upwards from 5.8, and struck at a depth of 155 kilometres (96 miles).
National broadcaster NHK said there were no immediate reports of any damage or injuries but it warned of the possibility of aftershocks and cautioned viewers to be careful.
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 nuclear facilities in the region hit by the quake avoided damage, including 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 resulting wave crashed into Japan's northeast, destroying vast swathes of the coastline and 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. However, strict building codes frequently mean that even powerful quakes that might wreak havoc in other countries can pass without much damage.