Here is a recent thread you may find helpful. It was primarily about a hair washing phobia, but general bath fears were also discussed.
http://www.autism-pdd.net/forum/forum_posts.asp?TID=17995&am p;am p;KW=allegra

My son goes through anti-bath phases occasionally. They usually last a few weeks. I just set up the plastic pool outside and see if he will go "swimming" after dinner. Or else I just do the 2 minute bath...screaming and all...
How is his communication? When my son was 5y--we moved to a new house. He was fine taking his baths like always--loved them! Out of the blue, he decided to hate it! We could not figure out why he was having such a fear. He wouldn't do showers either. It lasted for a month. He could never answer our questions about why he was scared. Finally, he got the words out and said that he was scared of falling thru to the other floor. (Bathroom upstairs). We only had lived in a single story house his whole life until this time. For some reason---he stopped the fear just as quick as it came on.........WEIRD!
It's important that you stay calm, so he doesn't start to further associate bathtime with emotional chaos and want to avoid it for that reason. You could also try a social story, explaining in a concrete, visual way that water is only uncomfortable on a new sore, not on healthy skin or sores with scabs.
You might want to read this excellent topic about phobias, if you haven't already:
http://www.autism-pdd.net/forum/forum_posts.asp?TID=18152&am p;KW=phobias
Good luck with everything.
My boys are both Water Babies,In fact around here a bath can be used as a reinforcer,One time, I filled Zach's pool with warm water and bubble bath, outside in the yard,he loved it.
Lots of water play is the only way I can think of to help.Try an empty pool with a bucket of warm water in the center provied lots of pouring cups, toys, sponges ect..This way he will feel more in control. You can also give Icecubes,waterballons,water guns ,bath fizzies ect...
Good Luck,Linda