Vanity Fair quoted sources as saying church officials contacted actresses who were Scientology members under the pretense of auditioning for a training video, and then asked their thoughts about Cruise.
A Scientologist who watched the videos said whoever dated Cruise would not only have to please the actor, but also "toe the line for Scientology."
In a statement to ABC News, the church denied the magazine's claims.
"The entire story is hogwash. There was no project, secret or otherwise, ever conducted by the Church to find a bride (audition or otherwise) for any member," the statement said. "No church members were 'used,' nor were they punished, nor silenced."
Vanity Fair said Nazanin Boniadi, an Iranian-born, London-raised actress, was chosen to date Cruise between November 2004 and January 2005. Cruise broke up with Boniadi through Scientology officials several months before he and actress Katie Holmes began dating, the magazine said.
He and Holmes recently divorced after five years of marriage.
Despite the church's denial, Oscar-winning writer-director Paul Haggis, a former Scientologist who is also Boniadi's friend, said Vanity Fair's story is true.
"Naz was embarrassed by her unwitting involvement in this incident and never wanted it to come out, so I kept silent," Haggis wrote in an e-mail published on ShowBiz411.com.
"I was deeply disturbed by how the highest ranking members of a church could so easily justify using one of their members; how they so callously punished her and then so effectively silenced her when it was done," the e-mail said.
Holmes has never been a member of the Church of Scientology.