Police will allege the boy travelled 90 minutes from his home to Christ The Good Shepherd Church where Bishop Mar Mari Emmanuel was delivering a livestreamed sermon on April 15 in Wakeley, western Sydney.

The boy was restrained by members of the public before he was arrested by police and taken to hospital for surgery on injuries to his hand.

AFP Commissioner Reece Kershaw said the boy's home was searched the next day where investigators seized "a number of items".

"After examination of the alleged offender's electronic devices and when other evidence was obtained, investigators sought to speak with the alleged offender following appropriate medical clearance," he said.

The boy was interviewed in hospital by investigators from the Joint Counter Terrorism Team on April 18 and charged with committing a terrorist act.

He has been refused bail and is expected to appear before a bedside court hearing on April 19.

Bishop Emmanuel was taken to hospital with lacerations to his head and another of the parish priests, Father Isaac Royel, was also injured after attempting to intervene, police said.

The alleged stabbing was declared a religiously motivated terrorist act by NSW Police Commissioner Karen Webb, launching a joint investigation with the AFP and ASIO.

Bishop Emmanuel spoke for the first time on April 18 to tell his followers he was fine and recovering quickly.

He also said he had forgiven and prayed for his alleged attacker, and called for calm.

"The Lord Jesus never said go out and fight in the street, never said to retaliate but to pray and this is what I'm asking everyone to do," he said.

Meanwhile police made their first arrest after violent scenes broke out outside the church as hundreds of people gathered after the alleged stabbing.

Dani Mansour from Doonside in Sydney's west was charged with riot, affray and destroy/damage property during a public disorder.

He was granted bail with strict conditions at court on April 18, where it was heard he had allegedly uploaded footage of himself kicking two police cars on Instagram.

Commissioner Webb said the teenager was not a member of the parish.

She said up to 50 people could be arrested in connection to the riot and called for anyone with information to contact police.

With Australian Associated Press