The US Geological Survey said the 7.8-magnitude earthquake was centred 874km (543 miles) from the Japanese capital, at a depth of more than 660km.
The earthquake struck at 20:30 local time (11:30 GMT). Buildings in the capital swayed for almost a minute as the quake built in intensity.
There are no reports of serious damage. No tsunami alert was issued.
However, Tokyo's fire department has received calls about people suffering injuries as a result of falls, broadcaster NHK said.
Reuters reports that services on the Shinkansen high speed train line between Tokyo and Osaka were briefly halted by a power cuts.
Some trains in Tokyo also stopped for safety checks, causing crowds of commuters to form around some of the city's busier stations.
Michiko Orita, a resident of the island of Hahajima, near the epicentre, told NHK: "It shook violently. Our Buddhist altar swayed sideways wildly.
"I have not experienced anything like that, so it was so frightening."
Naoki Hirata, of the University of Tokyo's earthquake research centre, said: "This was a very big quake... the shaking was felt over a broad area... fortunately, because it was deep, there is little danger of a tsunami."
Japan is one of the world's most seismically active nations.
In March 2011, a massive 9.0 magnitude quake started a tsunami that left nearly 20,000 people dead in north-eastern Japan and caused nuclear meltdowns at the Fukushima Dai-Ichi nuclear power plant.