Footage of a group of Muslims being shoved and dragged away by police while performing the sunset - or Maghrib - prayer outside Sydney Town Hall on Monday sparked widespread outrage.
NSW Police have confirmed a senior officer had agreed to let the praying finish before moving the men on.
"The senior officer was attempting to relay that message to other officers who were carrying out a move on direction during what was a noisy, dynamic and fast moving situation," a spokeswoman said.
"However, some worshippers were moved on before the message from the senior officer was able to be relayed."
Police Commissioner Mal Lanyon is still offering a qualified apology, saying the move on direction was not targeting any religion.
"I have apologised for any offence taken for interfering with that religious process," he said.
NSW Premier Chris Minns has repeatedly refused to apologise for the actions of police at Monday's protest, providing steadfast backing of police who forcibly dispersed the worshippers.
He has also stared down calls for an independent inquiry into police behaviour at the protest because it might imply the state's law enforcement watchdog was not fit for purpose.
"I genuinely believe NSW Police, their leadership, their regular officers, would never, ever have disrupted a prayer service," the premier said.
The leader of Monday's prayer, Sheikh Wesam Charkawi, said no citizen should need protection from the police, particularly while engaging in worship.
He said he had not been aware that any officer had been spoken to or that there had been any agreement.
"The only remedy to the situation must result in nothing short of an inquiry and consequences. The commissioner is ultimately responsible. Those who made the decisions must step down, resign or be removed from their position," he told AAP.
Barrister and former police officer Mahmud Hawila, who reportedly negotiated with officers during the protest, said police should release the body-worn video footage from those involved.
"Simple demands - 1. Release the footage. 2. Public apology. 3. Independent investigation," he said in a post on social media.
Monday's protest was organised by pro-Palestine groups to coincide with Mr Herzog's contentious visit to Australia.
The four-day trip was declared a major event, unlocking further police powers to move on activists across large parts of central Sydney and the eastern suburbs.
Officers were seen beating, pushing and pepper-spraying people at the protest, including medics, who said they were violently pushed while attempting to treat the injured.
Five people were taken to hospital after the rally, while nine people were charged.
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