I think it is relative. Everything in Japan is expensive.
One thing about owning cars in Japan is the inspection they do every two-three years is VERY expensive. I am assuming that taxi's must go through the same inspection for licensing.
Also getting a license is very expensive. My cousin flew to Vancouver, stayed 6 months, got a BC drivers license and moved back to Japan and TRANSFERED his license to a Japanese one and he did not have to be retested due to some mutual arrangement. He said it was about the same cost and he got a great vacation out of it as getting a driver's license in Japan.
Gas is very expensive and so is the insurance.
I'm sure those who are living there now can be more detailed about the cost of driving in Japan.