The bottom line is that any large earthquake to hit Tokyo would be extremely deadly:

Even with technological advances and new construction standards, officials say thousands would die if a 7.3-magnitude earthquake were to hit Tokyo with an epicenter in Tokyo Bay.

In 2003, Japan’s Central Disaster Management Council published predictions that as many as 11,000 people could be killed and 85,000 buildings destroyed, depending on the time of day and wind strength. About 1 million people would be without water, 1.6 million households would lose power and 1.2 million would lose gas, according to Japanese officials. They also predict that as many as 7 million people would be forced to evacuate the city.

In 2005, the Japanese government launched an initiative to lower those numbers by providing aid or tax breaks for work to strengthen homes and buildings against the quakes and by working on improving Tokyo’s clogged roadways to enable better emergency response.  [Stars & Stripes]

You can read more about earthquakes in Japan and how to survive an earthquake at the link.