Bert Fields called a Vanity Fair report, previewed on the magazine’s website, “long, boring and false”.
He said it was “a rehash of tired old lies” run in the supermarket tabloids.
Tom Cruise and his third wife Katie Holmes divorced in July this year.
The article, written for October’s edition of Vanity Fair, claimed the top-secret project was led by Shelly Miscaviage, the wife of Scientology leader David, in 2004.
Special correspondent Maureen Orth said she was told by “several sources” that actresses were quizzed by fellow Scientologists to find a suitable partner for Cruise, one of the organization’s most prominent proponents.
Actress Nazanin Boniadi, who was born in Iran and raised in the UK, told the magazine she was approached in 2004 and “audited”, before being selected to date Tom Cruise.
The article alleges their first date was conducted “with an entourage of Scientology aides”, but the relationship faltered after a few months and ended in 2005.
The Church of Scientology has spoken out against the feature in a statement.
“There was no project, secret or otherwise, ever conducted by the church to find a bride (via audition or otherwise) for any member of the church. Never.”
It claimed the magazine relied on a small group of “anti-Scientologists” for information, who had “shamelessly exploited Tom Cruise’s divorce by spreading false and invented tabloid stories.”
Vanity Fair says it stands by the story and has denied claims that it paid its sources.
Maureen Orth is a long-time contributor to the magazine, who has interviewed Vladimir Putin and Margaret Thatcher, as well as writing investigative articles about the allegations of sexual abuse levelled against pop star Michael Jackson.
Tom Cruise married Katie Holmes, with whom he has a daughter Suri, in an Italian castle in November 2006.
Katie Holmes filed for divorce at the end of June this year and the couple announced they had agreed a settlement several weeks later.
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