The NSW Police watchdog on Friday announced it was in the public interest to investigate police actions at a protest at Sydney Town Hall on Monday, including incidents of alleged misconduct.
The police response at the rally triggered widespread outrage after officers appeared to use indiscriminate and extreme force to disperse a crowd of thousands of people protesting against Isaac Herzog's four-day Australian tour.
Among the most controversial incidents, police shoved and dragged a group of Muslims performing the sunset prayer, despite a senior officer agreeing to allow the minutes-long prayer to conclude.
The police watchdog said it had received a significant number of complaints.
Its investigation would include hearings.
"The commission will obtain and review all available material, including video and phone footage, documents, records and other information including that held by the NSW Police Force," it said.
The investigation will provide political cover for Premier Chris Minns, who has resisted calls from community leaders and politicians - including within his own party - for an independent inquiry into police behaviour at the protest.
He had cited the commission as the appropriate body for such a probe.
The premier has also rejected demands to apologise for the actions of police and provided steadfast backing of officers involved in dispersing the worshippers.
Police on Friday blamed an internal communication breakdown for the violent disruption of the peaceful prayer.
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 also reiterated his apology for any offence taken, saying the forced dispersal was not targeting any religion.
Muslim leaders have urged him to make an unqualified public apology and take action against officers.
The leader of Monday's prayer, Sheikh Wesam Charkawi, said he was only made aware senior police had struck an agreement to allow the prayers after his group was shoved.
He said no citizen should require protection from the police.
"The only remedy to the situation must result in nothing short of an inquiry and consequences. The commissioner is ultimately responsible," he told AAP.
The policing response brought back memories of the 1978 street protest that was the genesis of the Sydney Gay and Lesbian Mardi Gras festival."I found myself reliving ... the horrors, violence, and trauma inflicted by police on the 78ers that night," said Peter de Waal, one of the 1978 protesters.
Meanwhile, police have charged a 45-year-old man with stalking Mr Herzog in Sydney.
The man allegedly filmed the Israeli leader's car and swore at him as the motorcade drove past in central Sydney on Monday.
The next day, the man repeatedly drove past a childcare centre in Bondi Junction before stopping and swearing at a security guard.
He is due to face court on March 4 on stalking, offensive manner and driving charges.
About 10,000 people rallied against Mr Herzog's visit in Melbourne on Thursday. A smaller protest was held outside Parliament House when the Israeli president visited Canberra on Wednesday.
Mr Herzog was invited by Prime Minister Anthony Albanese after the Bondi terror attack.
Both leaders have largely praised the visit, describing it as an opportunity to strengthen relations and advance discussions about the Middle East.
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