The 16-year-old is accused of travelling 90 minutes from his home to attack Bishop Mar Mari Emmanuel during a live-streamed sermon at Christ the Good Shepherd Church in Wakeley on Monday night.
Investigators from a joint counter-terrorism team, incorporating state and federal police and ASIO staff, interviewed the boy at his hospital bed on Thursday before charging him with committing a terrorist act.
The offence carries a maximum penalty of life imprisonment.
The teenager did not appear in person or via video link in Parramatta Children's Court during a brief mention of the case on Friday. He was refused bail at a scheduled bedside hearing in the hospital.
Bishop Mar Mari Emmanuel was allegedly stabbed during a church sermon. (HANDOUT/Christ of Good Shepherd Church)
A brief of evidence will be served when the matter returns to court on June 14.
The 16-year-old's lawyer Greg Scragg told the court he may seek an earlier date, having been instructed by the teenager's family that the boy had a long history of behaviour consistent with a mental illness or intellectual disability.
Mr Scragg described the teenager as a young person in need of help.
The boy had a history of intermittent psychological treatment from the age of five up until shortly before the alleged offence, he said.
His family requested a treating psychologist see their son to see whether or not he presents an ongoing risk of self harm, he added.
"We may seek to bring this matter back earlier if a question arises in relation to his treatment or assessment for those conditions whilst he's in custody," he told the Court.
The magistrate recommended the boy be assessed by JusticeHealth while in custody.
Also on Friday, Australian Federal Police Commissioner Reece Kershaw said investigators believed the attack met the criteria of a terrorist act, but he refused to go into further detail.
Authorities previously said the stabbing was declared an act of terror because of the teenager's suspected religious motivation.
Bishop Emmanuel was stabbed up to six times, causing serious lacerations to his head, while a priest was also injured in the attack.
The teenager allegedly made comments in Arabic that referred to insults against "my Prophet" before stabbing the bishop, who has publicly criticised Islam and other religions.
Leaders from the Lebanese Muslim community in Sydney have said the 16-year-old's family did not believe he had been radicalised online before the attack.
NSW Police are still hunting for as many as 50 people involved in a riot that unfolded after the incident at the Assyrian church.
Dozens of police were injured, their cars vandalised and a cohort of officers and paramedics were forced to shelter inside the place of worship, prompting religious leaders to call for calm.
NSW Police Commissioner Karen Webb and Australian Federal Police Commissioner Reece Kershaw. (Bianca De Marchi/AAP PHOTOS)
NSW Police Commissioner Karen Webb said extra police were out in force with a high-visibility operation "for as long as needed to reassure the community we are there to keep them safe".
"We have deployed extra officers since Monday night, particularly in southwest Sydney but across Sydney to patrol places of worship," she said.
In an audio message, Bishop Emmanuel said he forgave his attacker and called on his followers to obey the law.
"I need you to act Christ-like, the Lord Jesus never taught us to fight," he said in the message from hospital, shared on Thursday.
Dani Mansour, 19, from Doonside, was the first person to be charged over the public disorder incident.
The NSW government is also considering tougher knife-crime penalties with a push from police for fresh criminal offences for parents whose kids have been caught with weapons.
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