Lawyer Jeffrey K Riffer sent the letter on behalf of the church to Vanity Fair editor Graydon Carter before the inflammatory story hit the shelves.
"We are writing regarding your, your editor's and reporter's shoddy journalism, religious bigotry and potential legal liability arising out of Vanity Fair's upcoming story about the Tom Cruise divorce," the letter begins.
The letter goes on to undermine the writer, Maureen Orth, claiming she "hasn't the vaguest clue about the practice of Scientology", and that she was getting her information from "fringe hate sites and their webmasters".
The Church of Scientology used the letter to threaten legal action against the magazine on the grounds that the story is "defamatory" and "false".
Earlier this month, Tom Cruise's lawyer Bert Fields denied the story's claims on behalf of the 50-year-old actor, calling the piece a "rehash of tired old lies previously run in the supermarket tabloids".
The story claimed that high-ranking Scientology officials auditioned suitable partners for Tom in 2004, following his split with Nicole Kidman in 2001.
According to the piece, actress Nazanin Boniadi was scouted to be Tom's partner, with Katie Holmes eventually becoming the suitable candidate for the role of Tom's wife.
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