The alleged killer of Charlise Mutten told police the child's mother planned to take her and run off with her ex-partner hours after he initially blamed an unknown real estate agent for her disappearance, a court has heard.

Justin Laurens Stein, 33, is standing trial in the NSW Supreme Court accused of shooting his partner's daughter in the head and back with a stolen rifle.

The nine-year-old's body was found in a barrel on the banks of the Colo River on January 18, 2022.

Mr Stein has pleaded not guilty to her murder.

Court played second interview

On Friday, the jury watched Mr Stein's second interview with police on the day Charlise's mum, Kallista Mutten, reported her daughter missing on January 14, 2022.

Prosecutors previously told the court they believe Charlise was killed in the early hours of the morning on January 12, while alone with Mr Stein at his family's property in Mount Wilson.

In the recording, Mr Stein tells detectives "Kallista's been planning to take Charlise", and claimed that she was going to do a "runner" with the girl's biological father, who lived in Queensland.

The court heard Charlise was staying with her mother and Mr Stein over the Christmas break but was legally under the custody of her grandparents in Tweed Heads.

Mr Stein told police Kallista's "got a lot of issue when it comes to her mum and custody".

In his first interview with police, which took place only hours earlier, Mr Stein originally said he left Charlise at the Mount Wilson property with an unknown real estate agent on January 12, because the girl was too sick to get out of bed.

The court heard he left the child there while he drove to pick up Kallista Mutten, who had been staying at a caravan park in Lower Portland — a 90-minutes drive away from the Mount Wilson property.

But in the second interview, Mr Stein admits the first story about the real estate agent was a lie.

He told officers that Kallista Mutten "dumped" that version of events on him in a phone call just before he was asked to attend Penrith Police Station and make a statement about the disappearance.

The court heard Mr Stein changed his story to say that Charlise was actually alone with Kallista at the caravan park on the morning she went missing, while he was in Mount Wilson.

"I'm the one that's going to get f****d in something I'm genuinely not involved in," he said.

Accused quizzed about Charlise

In the second interview, Mr Stein is seen standing up out of his chair and pacing back and forth, which he said was because he hadn't received an injection to treat his heroin addiction.

He told officers he thought Charlise was left alone at the caravan park when he picked up her mum and they headed back to Mount Wilson on January 12.

"I didn't think about it… I wasn't happy she was [Kallista]," Mr Stein replied.

When asked by police whether he thought Charlise was still alive he responded "honestly, I do really think she's OK".

Mr Stein's defence barrister Carolyn Davenport SC previously told the jury her client had initially lied "to protect Kallista".

She told jurors Mr Stein does not deny attempting to dump the body but denies being the one that put Charlise in the barrel.

The jury had previously been shown CCTV footage from January 13, a day before Mr Stein was interviewed by police.

The prosecution allege that footage shows Mr Stein driving to different locations while towing a boat and with the body of Charlise Mutten in a barrel on the tray of his ute.

Crown Porsecutor Ken McKay SC said the accused was looking for somewhere to dump the body before eventually landing on pushing it off a ravine near the Colo river.

The trial continues.