Convenient Car rental shop everywhere in Japan
It seems like Care rental is more popular in Tokyo than other cities.
Because of maintain car is expensive in Tokyo include parking fees.
One of the biggest car rental company called "Nippon rent a car"
You can reserve by Internet or telephone or just go the the rental office.
At the time of reservation
You need to have a valid driver's license with your passport.
The license should be valid one in Japan to drive the rental vehicle. (it's depends on which drivers license you have, please check with your government)