Have you spoken to your teacher about it? It could be down to hand position and posture in general. Light's right though - I know way too many people who ended up with tendonitis (myself included) or carpel tunnel etc.

If it hurts, stop... or maybe just break your exercises up so you're not just running up and down scales for an hour... do 20 mins alternate picking practice, then 20 mins on chords, then 20 mins improvising over tunes - whatever... If you do the same thing over and over for an hour you're likely getting bored and maybe not getting as much out of it as you could.

Worth speaking to your teacher about though so he can take a look at your posture while playing - or you could try playing in front of a mirror.