Homeless people sleeping on the Flinders Street pavement were given more than two week's warning to move on, in order to clear the way for scaffolding required for redevelopment work at the station.

But this advance notice meant that by Wednesday morning around a dozen homeless had been joined by a group of protesters and activists – as well as a large contingent of media and bystanders.

Tensions at the site were high by the time dozens of police and council workers arrived before midday. "All of our people were down there," Cr Doyle told 3AW radio.

Police have since blamed the involvement of protesters for the violence, who were described by police as "regular starters at any far-left protest".

Of the five people arrested, for offences including assaulting police, only one was homeless.

Cr Doyle said he now believed council officers should have acted earlier, before the site became a "running sore of protest".

"I think maybe we left it too long," he said.

"I think we dealt that very fairly and honestly, for the last 2½ weeks we have been telling people that yesterday was the drop-dead date that the scaffolding had to go in.

"We did everything that would be part of the social compact to deal with people fairly and yet it still turned into a fiasco that required a major police exercise and a major city exercise.

"Maybe we move that line of engagement a little further forward."

Some of the Flinders Street Station rough sleepers moved into motels on Wednesday and have been under the impression they could only stay there for a couple of days before going back to the streets.

But Launch Housing, which is overseeing housing the city's homeless people, said all of those given motel accommodation could stay there until a more permanent solution could be worked out, such as a place in one of the 40 transitional units promised by the Andrews government.

Deputy chief executive Heather Holst said some people had so far refused crisis housing. "That's partly because there's a lot of information flying around from different people about it, so we are trying to get a clear conversation going," she said.

Before chaos broke out on Wednesday, Jonathan "Link" Hardy, a deaf aspiring bodybuilder who communicates using a pen and paper, wrote that he might move from Flinders Street if asked by police but "maybe when everyone leave I come back I'm not sure."

Homeless man Glen had been living with his dog Tonka outside the station for more than a month.

He was followed by a swarm of protesters, media cameras and people filming with their mobile phones when he packed up his three suitcases and left the camp following the arrival of special operations police.

He is now stationed outside St Paul's Cathedral.

"I look like an activist now because the professionals [protesters] brought banners and took over the joint," said the 32-year-old.

Lisa Peterson. Photo: Jesse Marlow

Homeless people's advocate Lisa Peterson, who was not involved in Wednesday's violence, condemned the action of protesters, some of who are believed to be from the Homeless Persons Union.

"I think there were only half a dozen homeless people here yet it's became circus. The community didn't need a circus," she said.

"We've been asking [for help] to get off the streets for almost a year, the sector and bureaucrats keep saying 'no' to every idea we give them.

"This is their failing every bit as much as the fault of the protesters but again it's the homeless community of Melbourne who will suffer and that's not fair."

Ms Peterson said there had been a marked drop off in public sympathy for the homeless in recent months during the intense attention on the Flinders Street camp - a phenomenon also observed by Ms Holst.

"More people are asking questions that seem to be based on fear [such as] 'Aren't they dangerous' 'Would they break up houses or assault neighbours' – that sort of stuff," Ms Holst said.

"I have been really taken aback about the amount of that sort of talk."

A number of the rough sleepers who had been sleeping at Flinders Street have been dispersed to other areas of the CBD – with some setting up on the opposite side of the road or near St Paul's Cathedral.

Cr Doyle said he expected to see homeless camps spring up again in the future.

"You will still see a few people around," Cr Doyle said.

"That's why I'm not a great advocate for move-on laws. We are not discharging these people to accommodation that is permanent and therefore they are going to come back."