While the damage of child abuse can last years, he says in an interview that the mental abuse of the Catholic Church's teachings could take longer to get over.
The God Delusion author talks about a woman who described being abused by a priest as "yucky", but who found it equally disturbing to be told by her Catholic parents that a Protestant friend who died would be roasting in hell.
"Horrible as sexual abuse no doubt was, the damage was arguably less than the long-term psychological damage inflicted by bringing the child up Catholic in the first place," he tells interviewer Mehdi Hasan.
Mr Hasan asks Dawkins, "You believe that being brought up as a Catholic is worse than being abused by a priest?"
Mr Dawkins then explains his position further: "There are shades of being abused by a priest, and I quoted an example of a woman in America who wrote to me saying that when she was seven years old she was sexually abused by a priest in his car. At the same time a friend of hers, also seven, who was of a Protestant family, died, and she was told that because her friend was Protestant she had gone to hell and will be roasting in hell forever. She told me of those two abuses, she got over the physical abuse; it was yucky but she got over it. But the mental abuse of being told about hell, she took years to get over."
His comments were criticised by former Tory MP and practising Catholic, Ann Widdecombe, who accused Dawkins of attention seeking.
"Dawkins doesn't know what to say next to get attention," she said. "No sane person would believe that being brought up in a force for good, in the Ten Commandments, in the Beatitudes, and in the Gospels can be worse than child abuse."