Your staff is testing various thing for you and recently they even tried going to the doctor in Japan!
So, in Tokyo, when you go to the doctor, you usually go to the clinic or the hospital. To me, it sounds dramatic and like some place you should go to only if you have something very bad, but here, it is normal!!
So first, they ask you to fill out a form with your symptoms and then you wait until they call you and ask you to go to a specific consultation room.
There, the doctor will ask you once again to explain your symptoms and a nurse is standing behind for a reason that is yet to be discovered. And you will have your diagnostic!
You have to go back in the waiting room for a while before getting your prescription! Also, please be aware that if you need an attestation for your school or your company, it is not free of charge!
As for the medecine, the pharmacy only gives you the amount of medecine you need, so you do not end up with boxes still half full that you always forget to bring back to the pharmacy. And as in most countries, you can choose the cheaper option, the generics.