Low-level acid, horse manure, glass bottles and a can of baked beans were among the "missiles" thrown at police and horses at the protest on Wednesday morning, Shane Patton said.
About 1200 protesters tried to block the entrance of the Melbourne Convention and Exhibition Centre to protest at the Land Forces weapons expo, with wheelie bins set on fire and thrown towards a barricade of officers.
Thirty-nine people were arrested and charged with offences including assaulting, hindering and obstructing police, arson and blocking roadways, the police commissioner said.
Twenty-four police received medical treatment after being pelted with rocks, manure and acid by anti-war protesters.
"They come here to protest against anti-war, so presumably, anti-violence," Mr Patton said.
"The only way I can describe them is a bunch of hypocrites."
He said their conduct was "absolutely appalling".
"They were standing there in full-face balaclavas with ski masks on - there was no snow there," he said.
Police used pepper spray against the anti-war protesters. (Joel Carrett/AAP PHOTOS)
Trams were disrupted and major city roads closed as the commotion peaked with loud bangs ringing out across Melbourne's CBD when police pelted hundreds of protesters with tear gas and pepper spray.
Activists had earlier thrown eggs and water and yelled "war pigs" or "get a real job" at the expo's attendees as they walked along Yarra Promenade to enter the event.
"Shame on you, how does it feel to murder babies?" one group of protesters yelled in unison.
Rally organisers said the acid was butyric, a food additive, and protesters were met with a similar level of violence to police, leading to "eight to 10 times" the number of injuries to the activists.
"Police have attacked us with blows, kicks, boots on our throats, tear gas, pepper spray and rubber bullets," spokeswoman Caroline Da Silva said.
"We are expressing community anger in the only way that is available to us - on the streets."
Protesters and police have accused each other of using heavy-handed tactics. (Con Chronis/AAP PHOTOS)
Police defended their use of non-lethal control measures including rubber bullets, flash and smoke devices and tear gas on protesters, saying a large cohort was violent.
"We have conducted ourselves properly," Mr Patton said.
"I couldn't be prouder of the officers down there and to see the way they used restraint when confronted by people intent on provoking violence."
Police union secretary Wayne Gatt praised police officers for their commitment after being subjected to "filthy behaviour" by the protesters who had come to Melbourne to cause "havoc and anarchy".
Greens leader Ellen Sandell said she had written to the anti-corruption body calling for an independent inquiry into police tactics and "excessive use of force" at the protest.
Mr Patton slammed the Greens' accusations as "rubbish".
MP Gabrielle De Vietri, also from the Greens, attended the protest despite criticism from the premier and opposition leader.
The anti-war rally disrupted Melbourne's CBD as protesters and police clashed. (Joel Carrett/AAP PHOTOS)
Victorian Premier Jacinta Allan said the protest was "potentially dangerous and dynamic" while Prime Minister Anthony Albanese said police "should be respected at all times".
"People have a right to protest peacefully, but you don't say you're opposed to defence equipment by throwing things at police," he told Sunrise.
The protest was triggered by the government's stance on the conflict in the Middle East with many weapons on display at the convention used on civilians in Gaza, Disrupt Land Forces spokeswoman Jasmine Duff said.
Victoria Police expected the protest to be its biggest operation in more than two decades, with the cost between $10 million and $15 million.
The Land Forces International Land Defence Exposition, which will host senior international military, defence, government, scientific and industry delegations from around the world, continues until Friday.
