The New South Wales (NSW) Police watchdog will investigate allegations of misconduct against officers after violent clashes with crowds protesting a visit by the Israeli president this week.

The Law Enforcement Conduct Commission said it had decided it was in the public interest to investigate Monday's police operation after receiving a significant number of complaints.

Videos that emerged after the rally appeared to show police punching protesters and dragging away a group of praying Muslim men. A state MP was among those who said she was injured.

The NSW Police Commissioner has previously defended officers, saying they showed remarkable restraint after protesters refused directions.

The commission on Friday said it would review all available material, including video footage, and conduct hearings before delivering a public report to the state parliament.

Thousands of people attended the rally, protesting against Israeli President Isaac Herzog, who has been accused of inciting genocide against Palestinians in Gaza by a UN commission - which he denies.

Despite objections from pro-Palestinian groups, the government invited him to Australia after an antisemitic attack at Bondi Beach in December, saying it would help the Jewish community heal.

The Palestine Action Group (PAG), which organized Monday's protest, welcomed the investigation and called on Lanyon and NSW Premier Chris Minns to resign.

The police operation bore all the hallmarks of a police riot, targeting peaceful demonstrators, said Amal Naser. Genocide is a crime. Protest is not.

The Australian National Imams Council on Friday said the police conduct had not reflected the Australia we know and reiterated its demand for an apology.

The Australia Palestine Advocacy Network (APAN) said there must be transparency and consequences for wrongdoing, adding that the protest exposed a disturbing pattern of anti-Palestinian racism.

This is not only about one protest nor just about the Palestine justice movement - it is about the shrinking of democratic space and an attack on the fundamental freedoms of expression and peaceful assembly, said APAN's Katie Shammas.

Immediately after the Bondi attack, Minns introduced restrictions on protests, and ahead of Herzog's visit, announced additional major event powers effectively giving police authority to shut down areas of the city.

Monday's rally took place just half an hour after protesters lost a legal bid to overturn the major powers designation.

The rules allowed demonstrators to gather but forbade them from marching. Police say a number of melees broke out after crowds were ordered to move on from the area.

Twenty-seven people were arrested at the protest, and nine were later charged, while 10 officers were assaulted, police said.

In a statement, a NSW Police Force said it will work cooperatively with the watchdog inquiry.

The LECC is a strong and independent oversight body, and we respect this process, Police Minister Yasmin Catley said in a statement.

Minns has previously defended police actions, saying on Tuesday that police had been put in an impossible situation, urging the public not to look at a 10-second clip without the full context.

On Thursday, he refused to apologize to the Muslim community for police breaking up their prayer, saying he did not believe officers would have done so unless it was in the middle of a riot. Lanyon has apologized for any offence that may have been taken.

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