Despite showing international credit card logos, most ATMs in Japan do not seem to be linked up to the UK/US networks; this is also the case in many shops. I succesfully used my Visa at the bullet train ticket office in Japan, but not in Kyoto.
The best place to get cash is Citibank or 7-11 stores.
If you are travelling across the subway to take an express train, make sure you have enough cash before you start your journey, or always carry a contingency amount.