Violence that broke out when authorities moved a group of homeless people from outside Flinders Street Station was caused not by the homeless, but by protesters, police say.

Key points: A police officer was punched in violent protests at Flinders St

A police officer was punched in violent protests at Flinders St Police were moving on a homeless camp to make way for scaffolding

Police were moving on a homeless camp to make way for scaffolding Accommodation has been offered for three days for those moved

The group of about 20 homeless people was asked to leave to allow for the erection of scaffolding and building works at the station.

Acting Commander Stuart Bateson said five arrests were made during the operation, including one for drunkenness, one for assaulting police and the other for throwing an object at police.

He said one officer suffered minor injuries when he was punched in the back of the head by a protester.

People sleeping on the street outside the station have been offered three nights' accommodation at a motel in the city's northern suburbs.

The group of about 20 has been asked to leave to allow for building works. ( ABC News: James Dean )

Victoria Police Acting Commander Stuart Bateson said they had been given plenty of warning ahead of Wednesday's operation, and were largely cooperative.

"We would much rather be doing other things, but unfortunately this was what was required of us," he said.

"We've been talking to them about this work for some weeks and telling them that this work is coming.

"[We told them] we're not going to be able to accommodate rough sleeping and that work at the same time in the small space that's in Flinders Street.

"We spoke to them at around 10:30am [on Wednesday], and said we need to do this and most of them left, only a few remained, but unfortunately for us we had protesters come in behind the homeless and they gathered in relatively small numbers thankfully."

Activists joined the camp in the morning, holding signs and shouting "we want public housing".

The protesters said they wanted a more permanent option for the homeless camp.

Police remain on guard after removing homeless people from Flinders Street Station. ( ABC News: Karen Percy )

Protesters 'regular starters'

Acting Commander Bateson said the activists were known to police from previous protests.

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"They're our regular starters at any far-left protest, these are the people that we see on the lines regularly ... assaulting our members, yelling at our members, spitting on our members," he said.

"Thankfully, our police members are OK, they've had minor injuries, one was punched in the back of the head while he was on the line, but he was OK," he said.

Flinders Street was closed off for about an hour between Swanston and Elizabeth streets while the protest went on.

The commander said he did not know of any injuries to the protesters.

Earlier, Housing Minister Martin Foley said 15 people from the camp had already moved on, and four had gone into rehabilitation.

"There's a pathway out for the genuinely homeless and we would urge those protestors who have flocked to this in more recent days to cooperate with police let the workers get about their business and let's start restoring our fantastic Flinders Street railway station," he said.

The State Government last week announced a $9.8 million package to help clean up homelessness on the streets of Melbourne and move people into transitional housing.

Under the plan, 40 people would be given immediate transitional housing while new housing is built, and 30 new permanent modular homes would be built on public land by the end of the year.

Authorities recently attempted to remove the camp of homeless people outside Flinders Street Station who had spread their bedding and belongings across the footpath.