Justin Laurens Stein, 31, appeared via video link in Sydney's Central Local Court on Wednesday where his lawyer asked for an order to keep his client safe from other prisoners.
"Mr Stein (has) concerns for his personal safety while in custody," Paul Rowe said.
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 northwest 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.
Mr Rowe said Stein 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.
Magistrate Robert Williams said he could order Justice Health to assess the inmate's mental health needs and abide by any medication requirements.
But the magistrate said his prison status was up to Corrective Service NSW.
"I can't make an order for that," Mr Williams said.
The court was told the case, due back in court on March 18 in Penrith, involved some "complexities".
The 31-year-old was arrested at his Surry Hills unit on Tuesday night after police found the body of the child in a barrel while searching bushland near a stretch of the Colo River.
Stein was wearing a white hooded jumper and a blue surgical mask on Wednesday and did not apply for bail.
His court appearance comes after more than 100 police and emergency personnel - including dog units, homicide detectives, rescue choppers and volunteers from the SES and Rural Fire Service - scoured the area around Mount Wilson and bush near the Hawkesbury River for five days.
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