"The fact there were a number of groups of individuals after the protest that chose to act unlawfully is disappointing to us," he told reporters in Sydney on Sunday.
"Police aren't punching bags and don't deserve to have this happen."
Protesters clashed briefly with police at Central Station after the main rally about 6pm and pepper spray was deployed by officers after a group of people allegedly became aggressive.
Five people were treated at the scene after being sprayed.
Footage uploaded to social media appeared to show police ushering a group of protesters into the station from the street, after which some demonstrators begin chanting "no justice, no peace, police the police".
Mr Lanyon said several people were "inciting" police and when officers tried to settle the situation, a 21-year-old man allegedly acted aggressively towards them.
Officers from the riot squad attempted to remove him and a struggle ensued, police said.
The man was arrested with police alleging the group became more aggressive prompting officers to deploy pepper spray.
"I support the use of the capsicum spray and the way the police responded in order to ensure that there was no further violence," Mr Lanyon said.
"They acted professionally and took the appropriate action."
The 21-year-old Mt Druitt man was charged with offensive behaviour and resisting police.
He's been granted strict conditional bail to appear in Downing Centre Local Court on 27 August.
In a separate incident, officers tasered a 23-year-old man at Town Hall railway station after he scuffled with a 15-year-old boy and allegedly became aggressive towards police on Saturday afternoon.
The 23-year-old has been charged with affray and was due to appear at Parramatta Bail Court later on Sunday.
The 15-year-old, who knew the older man, was given a caution.
Crowds also rallied in Melbourne, Brisbane, Adelaide and some regional cities and towns in solidarity with US protesters angered by the death of African-American man George Floyd in police custody in Minneapolis.
They defied warnings from Prime Minister Scott Morrison and Australia's chief medical officer not to protest due to the coronavirus pandemic.
In Sydney, protesters waved signs saying "Police the police" and "Same s*** different soil", while the crowd chanted "I can't breathe", the final words uttered by Mr Floyd and 26-year-old Dunghutti man David Dungay Jr.
"They held my son down for 10 minutes," Leetona Dungay said of her son's death in Long Bay jail in 2015.
At 4.32pm, demonstrators knelt en masse in Sydney's Belmore Park and held a fist aloft to acknowledge the 432 Aboriginal people who have died in custody since 1991.