Vanity Fair recently claimed that Boniadi had been one of various actresses in an audition process for the role of Cruise's wife shortly before he went public with Katie Holmes.
Cruise's reps later strenuously denied the allegations, saying: "Lies in a different font are still lies - designed to sell magazines."
However, Haggis - who left the Church of Scientology in 2009 - has now written an email to Showbiz 411 claiming that the allegations are true.
Explaining that he has known Boniadi for three years and claiming that she has left the Church of Scientology, he said: "Naz was embarrassed by her unwitting involvement in this incident and never wanted it to come out, so I kept silent. However, 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.
"It wasn't just the threats; they actually made her feel ashamed, when all she had been was human and trusting."
Haggis added that people have a "fascination with celebrity" so will focus on this story, but claimed that "a number of people" involved with Scientology have been "treated shamefully".
He continued: "In Naz's case, she has no right to feel ashamed. She is not only a terrific actress at the beginning of a very promising career, she is a dedicated human rights activist and a truly lovely and caring person. The last thing she wanted or needed is this kind of publicity, but here it is, and I am sure she will deal with it with the same grace and dignity she exudes in her daily life.
"I'm appalled that any church would treat its parishioners this way, but Naz had never cast herself as a victim. She is strong and resilient and I am very proud to call her a friend."
Cruise's divorce from Holmes was finalised last month.