NSW Police Commissioner Mal Lanyon offered a qualified apology to Muslim groups but defended the actions of his officers as anger grows over police tactics and powers used to break up a protest rally on Monday.
Officers were seen beating, pushing and pepper-spraying people in Sydney, including medics, who said they were violently pushed while attempting to treat the injured.
Vision of a group of Muslims being disrupted while performing sunset prayers beside Sydney Town Hall prompted mass outcry.
"The police that had been confronted were moving forward to disperse everyone," Mr Lanyon told ABC radio on Thursday.
"This was not targeting any religion. I have apologised for an offence taken for interfering with that religious process, but it needs to be taken in context that we were moving a violent and aggressive crowd."
The powers that paved the way for the crackdown will be challenged in parliament after the protest against Israeli President Isaac Herzog's Australian visit.
Laws rushed through parliament after the Bondi terror attack allowed police to make a declaration that prevents people from seeking authorisation for rallies in key areas, leaving participants vulnerable to arrest for marching through the streets or obstructing traffic.
As a result, Monday's protest was a static gathering.
Mr Herzog's visit was also controversially declared a "major event", a designation protest organisers unsuccessfully challenged in court, unlocking further police powers to move on activists.
When the event concluded, demonstrators - some of whom only wanted to leave - could not move as police tried to stop the whole group from marching.
Officers soon began unleashing pepper spray and rushing at the crowd.
Street medic Omaim Al-Baghdadi was wearing a vest identifying herself as medical personnel when police arrived.
"We were trying to explain that we were doing treatments, but that didn't really register, so we got pushed and pulled," she told AAP.
"At the planter boxes, I found people laying down that were also injured, so I tried to commence treatment there, but again police came and pushed us quite violently."
That night, she treated other medics who had been caught in police tear gas while coughing up her own lungs.
Riley Brooke initially attended the event as a protester and was in the middle of applying first aid before attracting the attention of police.
"I was fully backed against the wall with my hands up and one hand on a water bottle, I think saying, 'I'm just flushing eyes out, I'm not in the protest anymore, I'm just doing first aid'," they said.
"One yanked me and threw me, and I fell flat down on the ground."
Premier Chris Minns has repeatedly defended the police actions but is facing calls from within his government for an independent inquiry into the handling of the protest.
Four Labor MPs have called on their leader to approve a review of the circumstances leading up to the clashes, held at arm's length from police.
Laws enabling protest crackdowns and the decision to not allow a court challenge to the laws until the end of the month should be probed, protest attendee and Labor MP Stephen Lawrence said.
Five people were taken to hospital after the protest and 27 arrested, with nine facing charges.
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