Holmes made the filing on Friday (June 29), with sources claiming that Cruise's approach to parenting and his strong ties to Scientology clashed with her own beliefs.
It was earlier reported that Holmes allegedly believes that the Church has had surveillance cameras and several vehicles tailing her in recent weeks.
However the organisation has released a statement via TMZ, stating that the reports are completely false.
The Dawson's Creek star and Cruise were married for five years and are parents to daughter Suri Cruise.
Holmes is currently pursuing full custody of the 6-year-old, whom she plans to raise in New York.
Photo gallery - Tom Cruise and Katie Holmes - their relationship in pictures:
Copyright: Rex Features