First port of call would really be to see a chiropodist or podiatrist. Take your skates with you. Explain the problem. You may find that some form of orthotic helps a lot. GPs are a bit general, really, to be of much help with this sort of thing and they tend to take the, "Well, stop doing what makes it worse, and everything is sorted," approach, which really isn't what you want!
It may be that orthotics sort the problem, it may be that you need your skates punched out or even different boots. The foot specialist will be the person to best advise.
Good luck!