I stand corrected on what I am about to write - it has been a while since we did potty training, but...
I seem to remember that when I was doing the research on how to potty train, this was actually quite common, and one of the reasons was the sound the poo made as it hit the water, so if you are getting him to sit on a normal loo, perhaps put a bit of toilet paper in first so the sound is not "scary'.
Another reason was they did not like to see parts of their body flushed down the loo - some children see their poo as still part of them, so you need to somehow get him to understand that that is where poo goes and he is not flushing part of himself away, or desensatize him to the process - get him to watch you putting the poo from his undies in the loo, wipe him a bit with toilet paper, before using wipes / wet cloth. Get him to flush the loo etc.
Explain the process of flushing - poo in loo, flush, water takes it away to the sewer (pipes under the ground) etc. Make a story of it and make it sound lie the poo is off on an adventure.