L.S.
My son did the same thing but it continued from 2 years of age until 4. I started him at 18 months in the water with me and he loved it. The next session he didn't want to go and kicked and screamed. This lasted for a few years. I tried several different sessions after that. Last summer he broke down and screamed and didn't want to go into the pool. He kept on "swimming" in the wading pool just fine on his own but didn't want to take the lessons. A few weeks after this he got in the big pool all by himself and since then we can't keep him out. This summer he did so well and now he is a little fish. I say just keep on trying but don't push it. The harder you push the more resistant he will be and possibly even more scared. As long as he still likes the water it will only take some time before he wants to go in full blast. I let my son get in the water when he was ready and this might help your son as well. Good luck!!
L.