Authorities have been fielding calls following the quake, but they say there have been no reports of major damage.
The earthquake disrupted public transport throughout the Metropolitan area. One train in Tokyo's Adachi Ward derailed after making an emergency stop, injuring at least three people.
Railway officials say bullet train services were suspended but later resumed. Trains on some local lines also stopped running.
Adachi Ward officials opened a public school gymnasium equipped with mattresses and blankets, allowing people who were unable to return home to stay overnight.
More than 30 people arrived within an hour of opening, including stranded train passengers.
The tremor ruptured water pipes in several neighborhoods.
Emergency crews rushed to a fire that broke out in a building outside the capital, and the wall of a building in northern Tokyo collapsed.
Officials are warning people to be wary of structural damage that may have already occurred.