Two mystery men were first spotted allegedly keeping watch on her at Tom Cruise's New York home - days BEFORE she filed for divorce from him.
And when Katie and daughter Suri, six, moved to a secret apartment in the Chelsea district of the city, the creepy pair suddenly appeared outside.
A source said: "About three days before the divorce was announced a Mercedes SUV was sitting outside Tom's apartment in Greenwich Village.
"They were sat about a hundred yards from the house - a couple of suspicious-looking characters in sunglasses.
"When Katie came out they tried to discreetly follow her. It was obvious they weren't paparazzi or Press.
"They looked like former military or police and were carrying a small pocket digital camera.
"Then when it emerged Katie had rented a new place in the Chelsea area they were watching that too." Katie believes the Church of Scientology is spying on her because it sees her as a threat in the wake of her break-up with Cruise - the cult's most famous believer.
© FameFlynet.uk.comMystery man at Holmes' flat
"Then police were called and went to the car to ask them what they were doing."
A second car - a white Cadillac SUV - has also been allegedly used to keep watch on Katie, 33.
It was yesterday parked at a bus stop directly outside the apartment building entrance - with four middle-aged men inside.
Asked what they were doing, one of the men replied: "We're waiting for someone off the bus."
When it was pointed out they had been there for days, he added: "They still haven't got off the bus."
Two other men - thought to be associates of the four in the car - were seen walking around the building taking pictures.
An NYPD patrol car later turned up and an officer said they had a report about a suspicious vehicle and were about to run a check on the Cadillac's number plate.
The Sun told yesterday how Katie ended her marriage to Mission: Impossible star Cruise because she did not want Suri raised in the cult.
She has filed for divorce in New York because she has a better chance of getting sole custody there than in California, where Scientology has more influence.
The source said: "Katie just wants the best for Suri. This is awful for her but she is being very brave. It's a terrifying situation for Katie.
Katie made her move now because Suri is six - the age at which Scientology takes a lead role in the education and religious teaching of children.
The actress believes Scientologists put investigators on her tail after realising her relationship with Cruise was breaking down.
The religion - set up by sci-fi writer L Ron Hubbard in 1953 - has previously been accused of harassing former members who try to break away.
© Splash NewsWho are you? ... New York cops question the men in the Mercedes
And former top-ranking Scientologist Marty Rathbun was allegedly harassed in his home.
Cruise himself is even reported to have been kept under surveillance during a period in which he distanced himself from the cult.
Batman Begins star Katie wed 49-year-old Cruise five years ago. She is his third wife.
Katie was raised as a Catholic. Yesterday locals in Katie's home town of Toledo, Ohio - where her parents still live - said they were delighted she was breaking away from Cruise and his cult. A family source said: "We're glad she's returning to our church.
"We're sad Katie faces becoming a single parent but we know she was overshadowed by Tom and didn't share his Scientology beliefs.
"She was raised a Catholic and no doubt she'll want to bring up Suri in the church of her childhood."
Scientology insiders claim the Church arranged their marriage and Katie was "auditioned" for the role of Cruise's wife. When they married in Italy, Scientology leader David Miscavige was the best man.
By Samantha Domingo, Ex-Scientologist
When Scientologist couples split up, the person who poses the biggest threat to the church becomes what is known as "Fair Game" - an enemy whose reputation can be destroyed.
In January 2009 - when I went public with my story - my ex-husband was ambushed by agents from the church's Office of Special Affairs.
He was told to deal with me and if he didn't, his new Scientologist girlfriend would lose her job within the church. The OSA also asked my ex to report back on my activities to them.
Thankfully he wouldn't hear of it and, as far as I know, he has cut his ties with Scientology.
The OSA is a ruthless force and certainly one of the murkiest aspects of Scientology.
BBC man 'stalked'
Creepy Scientologists made an investigative journalist go into meltdown with a campaign of brainwashing and stalking.
John Sweeney, 54, claims his team were constantly watched by shady men in black SUVs with tinted windows when he filmed a BBC Panorama documentary on the cult in 2007.
A mystery man kept tabs on them and it later emerged his Scientology handlers were reporting back every few minutes directly to cult leader David Miscavige. After being taken to an exhibition claiming psychiatrists set up the Holocaust, Sweeney launched into a furious tirade with a church spokesman.
He later apologised, claiming he lost his cool after weeks of being stalked. He also said Scientologists were "taking control of my mind".
The Church of Scientology, through law firm Carter Ruck, denied his team were followed.
Trading one cult for another. Way to go :/