(ABC News) -- Oscar-winning director and former Scientologist Paul Haggis supports Vanity Fair's story that actress Nazanin Boniadi was auditioned by the Church of Scientology to be Tom Cruise's real-life girlfriend.
In an email to ShowBiz411.com, Haggis says he has known Boniadi for three years.
"Naz was embarrassed by her unwitting involvement in this incident and never wanted it to come out, so I kept silent," Haggis wrote in the email published on the website Sunday. "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 Church of Scientology told ABC News in a statement today that "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 church also says, "No church members were 'used,' nor were they punished, nor silenced."
As for Haggis, Karin Pouw, a spokeswoman for the Church of Scientology International, said he is an "apostate." She told ABC News today that Haggis is "attempting to grab headlines and falsely slander his former religion."
In the October issue of Vanity Fair, special correspondent Maureen Orth writes that actresses were told they were auditioning for a training film, and asked, "What do you think of Tom Cruise?"
Orth, who interviewed "several sources," says the entire arrangement was headed by Shelly Miscavige, the wife of Scientology chief David Miscavige.
Marc Headley, a former Scientologist, told Vanity Fair that he saw those audition tapes when he was the head of the church's in-house production studio.
"We assumed that this was going to be for "Mission Impossible 3," and then I later found out that it was just an audition process to try and find a girlfriend for Tom Cruise," Headley told ABC News in July.
The Church of Scientology says Headley is a disgruntled former member of the church who they accused of embezzlement. Headley denied the allegations and no charges were filed.
Vanity Fair reports that "in a month-long preparation," Boniadi was "told to lose her braces, her red highlights and her boyfriend." The Iranian-born, London-raised actress even reportedly signed a confidentiality agreement and was told if she "messed up" she would be declared an enemy of Scientology, the magazine wrote.
ABC News reached out to Boniadi, but she has no statement or comments at this time.
Boniadi and Cruise first met in November 2004, according to the article. Boniadi, the magazine claims, "first sensed that this was possibly going to be an arranged marriage" and although they spent that first night together "they did not have sex."
Vanity Fair reported that Cruise told Boniadi, "I've never felt this way before," and eventually his affection became "overwhelming" for the actress. Cruise reportedly complained to Boniadi, "I get more love from an extra than from you," according to Vanity Fair.
The article claims that Boniadi moved into Cruise's home and was given a credit card issued in the name of his production company as her only source of money.
The relationship ended in January 2005, the magazine reported, just three months before Cruise appeared in public with Katie Holmes. The article claims that Cruise wanted "someone with her own power, like Nicole Kidman."
Boniadi, the magazine writes, was then reportedly sent to a Scientology center where she broke down and revealed her relationship with Cruise to a friend, which supposedly violated her confidentially agreement. As punishment, Vanity Fair says her chores included "scrubbing toilets with a toothbrush, cleaning tiles with acid and digging ditches in the middle of the night."
The Church of Scientology, however, denied this to the magazine, saying, "The Church does not punish people, especially in that way."
Following the reported failed relationship, Boniadi, 32, went on to appear in the soap opera "General Hospital" and had a role in the 2010 blockbuster film, "Iron Man." Boniadi is now a spokesperson for Amnesty International and no longer involved with Scientology, according to the magazine.
Holmes filed for divorce from Cruise earlier this year after six years of marriage. The couple has a 6-year-old daughter named Suri. Holmes did not become a Scientologist until she started dating Cruise. A rep for Holmes told ABC News that she has no comment on the story and it was done without Holmes' participation even though her face is on the cover of the issue.