My daughter was afraid of her bowel movements at first. It's odd that they notice a difference between going in a diaper and going on the toilet!
First of all, make sure he is comfortable. Does he have a special seat that you put on the toilet that fits his tiny bottom? Is he going in a different potty or using the big one?
If he is in a nice comfy seat, just tell him that it's ok to go potty. Have you noticed certain times of the day when he has his bowel movements or even certain faces or gestures he makes that suggests that he is about to go?
If you pay attention closely, you can pinpoint what happens to him right before he decides to go and whisk him away to the toilet before it's too late.
With my daughter, she would start crying and just needed to be consoled. I would rub her back to help her relax and tell her that it was going to be ok. To make it fun, and funny, I would tell her to talk to herself. She would tell her poop to come out of there and she went from crying about it, to laughing and having fun with it.
Stool softeners might help too. Some kids get scared simply because it is too hard for them to get out. My nephew actually held it in so much that he became constipated....all because he didn't want to sit on the toilet and go!
I hope your situation doesn't get to that point and that something I said can be of some help to you. Good luck!