A number of people also chained themselves to the rented vehicles that were draped in black and emblazoned with the web address of a vegan documentary.
The vans have since been towed away.
Those arrested could face charges relating to obstructing a roadway, and resisting police.
The action caused traffic chaos during the morning peak.
Protesters also gathered at abattoirs in Corio, Pakenham, Laverton North and Bacchus Marsh, as part of a national series of rallies.
Organiser and director of animal rights documentary, Dominion, Chris Delforce, said Monday's protest marked one year since his film's release.
"The industry is telling people these animals are being killed ethically, that they are being killed humanely - the reality is ... it's the furthest thing from humane," Mr Delforce told AAP.
He laughed off Prime Minister Scott Morrison's suggestion the protests occurring across the country were "un-Australian".
"I think most Australians are opposed to animal cruelty," he said.
It comes after the Gippy Goat Cafe in West Gippsland announced on Sunday it's closing its doors, blaming "nearly 4 months of constant harassment, vile statements and threats from the abusive vegan activists".
"We have personally been subjected to an appalling stream of threats of extreme violence against ourselves, our family, our staff and even their families," operators John and Penny said on Facebook.
"Eight good people are now without a job, families no longer can enjoy the good food and open space, and children can no longer interact with our animals," it said.
The operators said enforcement action was "ineffectual".
Mr Delforce said he was not involved in actions related to the Gippy Goat Cafe.
Victoria Police Superintendent David Clayton criticised the protesters for not consulting police before the event.
"Police are able to facilitate planned protests when we are engaged," he said.
"This lack of engagement puts the entire community at risk with road closures and delays to transport services."
The demonstration caused some city trams to stop running or be diverted.
"It's causing quite the headache for people," Public Transport Victoria's Georgia Main told 3AW.
It comes after hundreds of animal rights activists rallied on Saturday, as part of a global protest, calling for an end to slaughterhouses outside Queen Victoria Market.
Mr Morrison said the federal government would be open to supporting civil court action brought by pastoralists against the protesters.
"State and territory governments should ensure the full force of the law is brought against these green-collared criminals," the prime minister said.
Farmers were going through some of the toughest conditions in more than a century and should be supported, he added.
Activists arrested at NSW abattoir
Nine people have been arrested after chaining themselves to machinery in a NSW abattoir as part of a nationwide protest.
The animal rights activists chained themselves to a conveyor at Southern Meats about 2.30am on Monday, NSW Police said in a statement.
Police arrived at 4am but a rescue squad was required to cut the group free from the machine before they were arrested.
Three women refused to walk and were carried from the facility to a police vehicle.
Three men, one 46 and two aged 22, and six women, aged between 21 and 61, were taken to Goulburn Police Station to be charged.
The NSW abattoir has declined to comment.
Meanwhile in Sydney, about a dozen people dressed in black walked from Hyde Park to Martin Place on Monday morning as part of the co-ordinated national protest. The small group was escorted by police on their march.
Protest spokesperson Isy Veira said they are calling on state and federal agriculture ministers to listen to several demands, including adding an animal cruelty documentary to the school curriculum for kids over 15.
Despite the small numbers at the protest, Ms Veira was happy with the turnout.
"We've got riot police following us around so we're obviously shaking things up a bit," she told AAP.
"I think that protest and direct action and animal rights activism will continue until the demands in the statement are met.
"They aren't unreasonable demands, we're just asking for transparency and compassion."
Prime minister admonishes animal activists
The prime minister this morning has scolded the "shameful" actions of vegan protesters who have invaded farms and abattoirs.
"It is shameful, it is un-Australian," Mr Morrison told 2GB radio on Monday. "This is just another form of activism that I think runs against the national interest, and the national interest is being able to farm their own land."
While MP Bob Katter said he would be "instructing the Parliamentary draftsman today to start working up legislation which would make invasive and aggressive vegan activism illegal and punishable with jail time".
"Every Australian has the right to put forward his or her point of view - and heaven only knows I have been removed by the police in demonstrations against the coal seam gas, along with Alan Jones - but you have no right to impose your viewpoint upon other Australians and invade their privacy," he said.
And after about animal rights campaigners chained themselves to equipment at a Queensland abattoir, the prime minister expects the police to play a role.
"I'm expecting state governments - as I'm sure they will - to do their jobs," he said.
Up to 200 others remained outside the Warwick facility, protesting against what they said was the barbaric slaughter of sheep and pigs.
Brad King, from the activist group Farm Animal Rescue, was among those at the protest and said animals slaughtered at the site had endured terrifying deaths.
On Sunday, Queensland Agriculture Minister Mark Furner said he'd had a gutful of activists putting farms at risk.
He is drafting regulations that would allow police and agriculture ministers to slap protesters with on-the-spot fines.