About 30 men from the National Socialist Movement marched along Spring Street at an anti-transgender rights rally on Saturday afternoon.
The black-dressed group repeatedly performed the Nazi salute and held signs calling transgender people offensive names, leading to violent clashes with hundreds of counter protesters.
In an Australian-first, Victoria banned the public display of the Nazi swastika last year.
Attorney-General Jaclyn Symes and Multicultural Affairs Minister Colin Brooks are looking at what further action the Victorian government can take to address Saturday's "disgraceful" scenes, Deputy Premier Jacinta Allan said.
"The government has absolutely no tolerance for this sort of behaviour and we'll continue to work very, very hard to address what sits behind those sorts of disgraceful actions," she told reporters on Sunday.
Mr Brooks said the Andrews government will review the Racial and Religious Tolerance Act as it works to "pull the noxious weed of Nazism out by the roots".
"Not just the heads of the root ... by dealing with the symbols and the gestures," he said.
"As important as that work is and we'll continue to look at ways to do that, this is a real insidious hateful ideology, and we need to deal with the root causes of it."
Officers prevented a brawl between the groups and were powerless to stop the actions of the neo-Nazis, Police Association of Victoria secretary Wayne Gatt said.
He said Victoria could ban the salute but people hellbent on causing outrage would find a replacement, raising the question of whether the government should outlaw neo-Nazi groups altogether.
"What we've seen is far-right extremism around the world lead to a new form of terrorism," Mr Gatt told Melbourne radio station 3AW.
"We've seen that in New Zealand. We've seen that in many other parts of the world. And, indeed, unchecked in Australia it will have the same effect."
Spring Street and the surrounding area were blocked to traffic for several hours as police, including mounted officers, tried to keep the protesters separated.
Three people were arrested, including a 22-year-old Point Cook man for allegedly putting a female officer in a headlock and taking her to the ground and a 23-year-old Thornbury woman for allegedly slapping a police officer on the neck.
Both are expected to be charged with numerous offences including assaulting police. The two officers were uninjured.
Vision of an arrest posted to social media appears to show a police officer twice knee a prone protester in the back.
In a statement, Victoria Police said it was aware of the vision but no complaint had been received over the arrest.
Liberal MP Moira Deeming, who was photographed at the rally with organiser and British anti-trans activist Kellie-Jay Keen-Minshull, said she was disappointed Victoria Police let the masked men into the buffer zone.
"Police managed to stop hordes of TRAs (trans rights activists), but somehow could only walk masked men past us (sic) they did a horrible Nazi salute," she tweeted.
Federal Labor MP Josh Burns described it as an "ugly alliance" and said the brazen marching with Nazi salutes was unacceptable.
"This is a time for us to consider whether tougher laws are needed," he said.
In a joint statement with LGBTQI+, multicultural, women's and other groups, Equality Australia chief executive Anna Brown suggested neo-Nazi and anti-trans ideologies have much in common.
"They target vulnerable minorities to incite hatred and fear," she said.
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