Their presence has sparked reports that they are Scientology operatives, hired to follow Holmes after her surprise divorce filing from Tom Cruise.
But sources close to the situation say the men aren't related to Scientology at all – they're actually a new security team hired by Holmes herself.
The Church of Scientology has also denied having Holmes, 33, followed. "There is no truth whatsoever to the [report] that the Church of Scientology has sent anyone to follow or surveil Katie Holmes," Gary S. Soter, an attorney from the church, said in a statement.
Holmes rented the three-bedroom Manhattan apartment in the weeks leading up to her shocking move to divorce Cruise, who is currently filming in Iceland and turns 50 on Tuesday. The actor is a passionate advocate for Scientology, a religion that Holmes (who was raised Catholic) embraced at the start of their relationship.
But Scientology may become a hot-button issue in their split. Holmes reportedly filed for sole legal custody of their daughter Suri, which would give the actress the power to make decisions on the 6-year-old's education and religion choices.
Holmes "has always been more of a Catholic than a Scientologist," a source tells PEOPLE in the magazine's new cover story about the split.
For much more about Holmes and Cruise's divorce, Suri's future and the role Scientology will play, pick up the new issue of PEOPLE, on newsstands now