There are indeed several clinics in the Tokyo metropolitan area where these examinations are done, it is more dependent on the date of the examination due to the availability of slots. Initial examinations (pre employment ) might not even be done in Japan, I had mine done in Alaska for example. My recommendation would be to get in touch with the contract agency and try to figure out where it is going to be because there is a very high probability that it won't be in the same place where upspeed had his done.