Cruise, who is suing a magazine for claiming that he abandoned his daughter Suri after the divorce, revealed this during a court deposition.
When asked by the lawyers if Holmes left him "in part to protect Suri from Scientology", the actor became angry.
"Listen, I find that question offensive. I find it, those statements offensive. Like with any relationship, there are many different levels to it. You know, I, I find it very offensive. There is no need to protect my daughter from my religion," Cruise said, according to the papers obtained by Radar Online.
Cruise said, "Did she say that? That was one of the assertions, yes."
When asked if Suri is "currently practicing Scientology," Cruise said, "No."
Holmes split from Cruise last year.