Terence Darrell Kelly, 36, was shackled and accompanied by armed riot squad guards when he boarded a charter flight that departed Carnarvon Airport shortly before midday on Friday.
WA’s Department of Justice confirmed Kelly would be escorted by special operations officers to a maximum-security facility in Perth.
Kelly appeared before a magistrate in Carnarvon on Thursday charged with various offences including forcibly taking a child under 16.
He was remanded in custody ahead of the matter returning to court next month.
Kelly, who is alleged to have acted alone and is yet to enter a plea to his charges, has no connection to Cleo’s family.
He was not on a list of known sex offenders in Carnarvon, a small coastal town almost 1000km north of Perth which does not have its own prison.
Police Commissioner Chris Dawson said Kelly would be subject to extra security measures “for obvious reasons”, having twice been hospitalised after self-harming while in custody.
Cleo was found alive and well early on Wednesday, 18 days after she went missing from her family’s tent at the remote Blowholes campsite.
She was rescued from a property just minutes from her family home in Carnarvon, about 75km south of the campsite.
Police forced entry to the home and found Cleo alone in a room, physically unharmed and playing with toys.
Kelly was arrested on a nearby street around the same time.
Family and neighbours of Kelly have told the ABC his image appears on a social media account that posts about loving children’s dolls and claiming to have a partner and children, despite living alone.
On January 27 this year, a post said he had warned his children, of which he claimed to have five, about online safety.
The profile also shares videos of a child in a bathing suit, captioned “my princess”, and another of a boy sitting on a couch, captioned “my son in Western Australia, miss you big boy”.
Cleo was pictured smiling in the arms of her mother Ellie Smith on Thursday when she was set to speak to specialist child interviewers for the first time.
Homicide detective Cameron Blaine, who was among Cleo’s rescuers, said she appeared to be holding up well.
“I can only see her from the outside. But from that point of view, I’m amazed that she seems to be so well adjusted and happy,” he said.
“It was really heartwarming to see that she’s still bubbly and she’s laughing.
“She’s falling asleep in her mother’s arms. There was one occasion where she asked if she could lay next to mum and have Ellie look at her while she fell asleep.
“It’s really good to see that she’s adjusted, she’s getting some sleep, she’s playing in the backyard exactly how you would expect.”
Police are yet to confirm whether Cleo was kept at other locations while she was apart from her family and have been tight-lipped on the exact intelligence that led officers to her location.
They had been seeking the driver of a car that was seen leaving the Blowholes campsite around the time she was allegedly taken.Jump to next article