Police were called to the Christ the Good Shepherd Church at Wakeley, in Sydney's west, about 7pm on Monday after Bishop Mar Mari Emmanuel was stabbed during a live-streamed sermon.
A priest from the Assyrian church was also injured after trying to intervene.
A 16-year-old boy was arrested over the attack, which has been declared a terrorist act due to the suspected religious motivation.
But the situation soon turned even uglier as a growing crowd turned on police and paramedics, who were forced to shelter inside the church for several hours after their attempt to extract the injured alleged attacker.
NSW Police Commissioner Karen Webb on Tuesday said a separate strike force had been formed to investigate the riot and it would run in conjunction to a probe into the stabbings.
Bricks, concrete and fence palings were used to attack police and damage equipment, injuring officers and rendering vehicles unusable.
"That is unacceptable and those that were involved in that riot can expect a knock at the door," Ms Webb said.
"We will find you and we will come and arrest you."
NSW Police Commissioner Karen Webb says a strike force has been formed to investigate the riot. (Bianca De Marchi/AAP PHOTOS)
Paramedics assessed and treated 30 patients, with seven taken to hospital, NSW Ambulance commissioner Dominic Morgan said.
"This was a rapidly evolving situation where the crowds went from 50 to a number of hundreds of people in a very rapid period of time," he said.
"Our paramedics became directly under threat ... and had to retreat into the church."
Prime Minister Anthony Albanese said people should let police and security agencies do their job rather than taking the law into their own hands.
"It is not acceptable to impede and injure police doing their duty or to damage police vehicles in a way that we saw last night," he said.
NSW Premier Chris Minns said faith leaders across western Sydney were denouncing the violence to quell any potential retaliatory attacks.
"Their message to their communities was universal and identical, and that is that they deplore violence in all forms ... and most importantly, that people remain calm during this obviously distressing period," he said.
More police could be deployed in response to the "obviously combustible situation", Mr Minns said.
"But our hope is that it doesn't come to that, and that common sense prevails, the community remains calm, and we let police get on with the job of investigating a major, major terrorism investigation."
Opposition Leader Mark Speakman supported the call for calm.
"The scenes we saw last night have no place in NSW," he said.
