Police have charged 39 people after a vegan protest shut down one of Melbourne's busiest intersections during peak hour, disrupting tram routes and forcing ambulances to be rerouted.

Key points: Protesters have been charged with resisting and obstructing police and obstructing roadways

Protesters have been charged with resisting and obstructing police and obstructing roadways Two 17-year-olds and a 15-year-old are among those charged by police

Two 17-year-olds and a 15-year-old are among those charged by police The demonstration brought 11 tram routes to a standstill during peak hour

Protesters chained themselves to three vehicles which were used to block the intersection of Flinders and Swanston streets this morning, Victoria Police said.

The disruptions caused significant delays for many commuters, who had already braced themselves for travel pain as buses replaced trains on five of the city's busiest lines as well as Gippsland V/Line services for a construction blitz.

Superintendent David Clayton said the protesters had not discussed their plans with police and put community safety at risk with "many people" unable to access vital services.

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"There are five major trauma hospitals in the CBD, ambulances needed to be rerouted because of those intersections being closed," he said.

"The lack of prior engagement is really disappointing. It places the community at risk and impacts on the safety of the CBD."

Two 17-year-olds and a 15-year-old were among 39 people arrested and charged with resisting and obstructing police and obstructing a roadway.

Police removed the protesters from the intersection about 9:00am. ( AAP: Ellen Smith )

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Superintendent Clayton said those charged had been bailed to appear in court at a later date.

The demonstration was one of several animal rights protests taking place around the country to promote a documentary about Australian livestock farm practices.

Police had also monitored protests at Laverton, Pakenham, Corio and the Melbourne Aquarium, Superintendent Clayton said.

He also noted that the sudden closure of an intersection of Melbourne's CBD had sparked "alarm" from people concerned an attack had taken place.

'Now I'm super late'

The protest, which began about 7:00am, brought trams on routes 1, 3, 5, 6, 16, 64, 67 72 35, 70 and 75 to a standstill.

Trams have since resumed.

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The tram corridor running along Swanston Street and St Kilda Road is the busiest in the world.

Buses replacing trains on the Caulfield-Pakenham line were also caught up in the traffic snarls caused by the protests.

PTV's Georgia Main said at one point the buses were unable to turn around at the Art Centre because of the heavy traffic, causing significant delays.

Joshua Keegan travelled from South Morang on a replacement bus then ran for a tram which he then found out was delayed.

"I'm late for my singing lesson and uni," Mr Keegan said.

Joshua Keegan said the protest made him late for university. ( ABC News: Zalika Rizmal )

"I finally got to Flinders Street Station and the tram I'm supposed to jump on was delayed because of vegans protesting about meat.

"It's been a massive delay and then to get to Flinders Street and my tram's not there, now I'm super late."

Landscape gardener Collin Fernandez was running half an hour late for work because of the transport disruptions.

"I've had to walk to a different station and wait for my tram there," Mr Fernandez said.

Colin Fernandez said he was not interested in veganism. ( ABC News: Zalika Rizmal )

He said while he recognised the activists' right to protest he was not interested in getting involved in their cause.

"If that what makes them happy, then go for gold," he said.

The protest forced northbound trams to terminate at the Arts Centre. ( ABC News: Zalika Rizmal )

In a separate demonstration, a group of about 50 activists gathered outside the Melbourne Aquarium, blocking off the main entrance.

Some linked arms by placing their hands in plastic pipes.

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The aquarium remained open, with visitors ushered through a side entrance.

'We want people to go vegan'

Vegan Rising campaign director Kristin Leigh said the Flinders St protest was one of nine planned around the country, including five in Victoria.

"We want people to go vegan, we want people to stop supporting animal abuse," Ms Leigh said.

"I don't believe any good person supports what's happening in slaughterhouses and so-called farms today, these are places of exploitation of innocent vulnerable beings.

"Animals are suffering in ways that most of us could never imagine. It's not about bigger cages, it's about animal liberation."

Animal rights activists blocked cars and trams outside Flinders Street Station. ( ABC News: James Oaten )

Roads Minister Jaala Pulford was critical of the methods used by the protesters.

"This is not an effective way to be making this point," Ms Pulford said.

"I don't know that there's a cause that ever gained more support by making people late to work.

"We do respect people's right to protest but there's little to be gained I think by just upsetting a whole lot of people just trying to get about their day."

Protests follow closure of goat farm cafe

The protests come a day after the owner of a cafe at a goat dairy farm in Gippsland said he had been forced to shut down his business after four months of "harassment" by animal rights activists.

The Gippy Goat Cafe closed its doors on Sunday after owner John Gommans said his business had been targeted for more than three months by activists.

John and Penny Gommans have closed their West Gippsland cafe. ( Supplied: John Gommans )

"We've decided that we've had enough. Every second phone call at the cafe was harassing our staff and telling them that we were such terrible, terrible people, to go and get a better job," he said.

Mr Gommans said customers who posted photos of themselves at the farm on social media were also targeted.

"People would post that on the Facebook page, just to receive a barrage of horrible emails," he said.

He said he believed the animal rights website Aussie Farms was connected to some of the harassment his cafe had received.

In a statement, the group's executive director, Chris Delforce, said his organisation had published footage taken inside a facility where male goats were "bludgeoned to death".

"I suspect this knowledge becoming public has negatively impacted their business more than the actions of individual activists," Mr Delforce said.

He said he understood there had been harassment levelled at activists by supporters of the cafe.