Justin Laurens Stein, 33, has pleaded not guilty to murdering the schoolgirl on or around January 12, 2022, at Mount Wilson, in the Blue Mountains west of Sydney.

His lawyer told a trial in the NSW Supreme Court earlier this week it was Charlise’s mother, Kallista Mutten, who had shot the girl, not him.

At the time of Charlise’s death, Ms Mutten and Stein were in a relationship after meeting while both were serving jail time.

Ms Mutten called police at 8.12am on January 14 to report her daughter missing, a recording of which was played to the jury on Wednesday.

“I’m sorry, I need to report my daughter missing – she’s nine,” a sobbing Ms Mutten told the operator.

In an at-times jumbled account of what occurred, she said the last time she saw her daughter was two nights earlier and she had left the girl with Stein.

Charlise had been visiting the couple over the holiday break, with the group spending time between a property at Mount Wilson and a caravan at the Riverview Ski Park, about 90 minutes away.

“She was here and I wasn’t here, my partner was here … during the morning she was sort of sick, so she was sort of lethargic and I was two-and-a-half hours away,” Ms Mutten said in the call.

She told the operator that Stein had left Charlise, who he claimed was sick, with a woman who had come to do a valuation of the 12-acre Mount Wilson property, which was owned by his mother.

“He asked if she could mind her while he went and got me … he didn’t want her in the car because she’d been throwing up,” Ms Mutten said.

“When we got back they were gone.”

Crown prosecutor Ken McKay SC earlier told the jury that Charlise being sick and remaining with the property-valuer was one of two explanations Stein gave Ms Mutten about what happened to her daughter.

He would later suggest the nine-year-old might have been taken by people from his criminal past.

The officer in charge of the investigation, Detective Sergeant Bradley Gardiner, started giving evidence on Wednesday and he is expected to remain in the witness box for the rest of the week.

He confirmed that during the probe into Charlise’s death police learned Ms Mutten was pregnant with Stein’s child.

Charlise travelled from the Gold Coast to Sydney as an unaccompanied minor in December 2021 with plans to spend Christmas and New Year’s Eve with her mother and Stein.

On the evening of January 12, Charlise travelled back to Mount Wilson with Stein alone, while Ms Mutten remained at the caravan, prosecutors said.

CCTV images captured the 33-year-old at a service station the next day towing a boat with his Holden Colorado ute, which was also allegedly transporting a barrel containing Charlise’s body.

The barrel was found near the Colo River, northwest of Sydney, on January 18.

She had been shot once in the head and once in the lower back.