this is one of those times when it would be so nice to see a video! there are so many things that could be going on...
1. is he green over fences and learning how to canter them?
2. is he hurting anywhere?
3. are you anticipating a refusal when you canter in?
4. have you ever accidently hit him in the mouth/back when you canter in?
5. is he afraid?
6. are you afraid?
Horses will stop because of pain, fear, or a learned habit. Assuming that this is purely an attitude thing and not a physical or 'green' issue... I'd start off by cantering lots and lots of poles on the ground so he gets used to steping over something in his canter stride. Then i would suggest making a jump that's very small. (like, a tiny crossbar he can easily step over) Then canter towards it with your legs long, seat deep, staring intently at the jump. Basically wtih your entire body say "jump it". Your eyes should always be on the top rail (never at the bottom of the fence) until right before the fence you look past it. If you feel him at all ask the question "are you sure" (hesitates even slightly, barely slows his pace, lifts his head, looks somewhere else, etc), close your leg on. It is very important that your hands are independant from your body because as he goes to the jump you can't let him look left or right! If he stops, his nose better be pointed straight in front of him, in front of the fence. If he stops, force him to go over it, even at a stand still if that's where he's at (it's tiny, he can do it). If he's going to jump it from a stand still grab mane as he goes over so you don't hit him in the mouth. Do it over and over again. Give him huge praise once he gets over. Also I'd suggest always cantering as soon as he lands (regardless of whether he steps over it or just kind of trots over). That way he learns that after the jump is always a time to be forward (not fast, forward).