A Sydney man charged with murdering a nine-year-old girl whose body was found in a barrel has been under long-term care for mental health problems, a court has been told.

Justin Laurens Stein, 31, appeared via video link in Sydney’s Central Local Court on Wednesday where his lawyer asked magistrate Robert Williams for an order to “protect his personal safety”.

Mr Stein is accused of murdering the schoolgirl, who was reported missing last week while holidaying with family at Wildenstein Private Gardens in Mount Wilson, a village in the Blue Mountains north-west of Sydney.

According to court documents the girl – who can no longer be named for legal reasons – was murdered between 7pm on January 11, and 10am on January 12 at Mount Wilson.

She was reported missing on Friday morning, January 14.

A police roadblock near the Wildenstein gardens in the Blue Mountains. Photo: AAP

Mr Stein’s lawyer said his client had been under long-term care for “mental health problems” and had been prescribed a fairly high dose of antipsychotic drugs quetiapine and risperidone for many years.

The magistrate said he would order Justice Health to assess Mr Stein’s mental health needs but that his prison status was up to Corrective Services NSW.

The court was told the case, due back in court on March 18 in Penrith, involved some “complexities”.

Mr Stein was arrested at his Surry Hills unit on Tuesday night after police found the body of a child in a barrel while searching bushland near a stretch of the Colo River.

The body is yet to be formally identified, but police say the remains are consistent with the girl who was reported missing from Wildenstein.

NSW Police Deputy Commissioner Dave Hudson said police had set up a crime scene and were still uncertain of exactly what happened.

He said police will allege Mr Stein put the girl’s body into the barrel.

“What we are sure of is that the accused that we charged with murder was responsible for, firstly, placing her in the barrel, and then disposing of that barrel in the bushland where she was located,” he said on Wednesday.

“Things will unravel over the next week or so to find a cause of death, the purpose for a death, and try and identify exactly what happened so that the remaining family have some comfort in that.”

More than 100 police and emergency personnel – including dog units, homicide detectives, rescue choppers and volunteers from the SES and Rural Fire Service – have been scouring the area around Mount Wilson and bush near the Hawkesbury River in a desperate search for the girl since Friday.

NSW Deputy Premier and Police Minister Police Paul Toole described the outcome of the search as “horrific”.

He said the hundreds of people involved had never given up, despite often working in torrential rain.

“They never gave up hope. People across this country have been hoping and praying for a good outcome,” he said.

“Today’s news is not what we wanted to hear. I mean this is horrible. This is horrific. This is shocking.”

The girl’s mother is being treated in hospital after suffering a medical episode after her daughter’s disappearance.

Police are yet to interview her.

“It has been difficult to approach and contact her but at some stage hopefully when doctors allow, we will be talking further with her,” Deputy Commissioner Hudson said.

The girl’s biological father revealed his heartbreak in a social media post on Wednesday.

“Goodbye you beautiful little girl. I love you so much. I miss you every day! You have captured the hearts of the nation and the world, and now those hearts are breaking, with mine,” he wrote on Facebook.

“This doesn’t happen! Kids need to be safe. What is wrong with you people????

“We will get the answers for you baby, and we will honour you properly. This is not the end of you or your story.”

The little girl’s school also released a statement on Wednesday, saying it was “devastated” and would offer support to students and staff.

“We are absolutely devastated to hear this morning’s news,” the statement said.

“Our hearts go out to her family, we cannot begin to imagine the distress they must feel.”

-with AAP