The latest temblor swayed buildings in the capital.
The US Geological Survey says the temblor had a magnitude of 6.2 and struck at 10:26 a.m. (local time) today.
It was centered about 179 kilometres east of Tokyo, at a depth of 24.5 kilometres.
Japan's northeastern coast was battered Friday by a magnitude 8.9 quake, the largest on record in Japan, and an ensuing tsunami that washed over hundreds of kilometres of coastline, causing widespread destruction.
Japan has been rattled by more than 150 aftershocks since Friday's massive quake.
Deccan Herald is on WhatsApp Channels | Join now for Breaking News & Editor's Picks