The head of Australian Border Force has admitted the agency's statement on an operation in Melbourne was "clumsily" written and has been misconstrued.

A statement released earlier on Friday said officers attached to Operation Fortitude would be in positions around the CBD this weekend "speaking with any individuals we cross paths with" about visas.

But ABF Commissioner Roman Quaedvlieg later told reporters in Canberra the press release was "clumsily worded" and did not properly portray the agreed role between Victoria Police and the Force.

Mr Quaedvlieg said Immigration Minister Peter Dutton had no knowledge of the press release and his office was not involved.

He said it was circulated at a regional level in Victoria.

"I didn't see it," he told reporters in Canberra.

Asked if any action would be taken against the media release's author, Mr Quaedvlieg said it was an internal matter which he would not canvas.

"It is an unfortunate incident," he said.

"It shouldn't have occurred. Remediation will be put into place but it's not a fatal embarrassment."

Mr Quaedvlieg said he had talked on Friday with Victoria Police Chief Commissioner Graham Ashton.

"We are good colleagues," he said.

"We have good institutional relationships. That's as far as I am going to take that conversation."

Cancelled less than 12 hours after being announced

Victoria Police cancelled this weekend's Operation Fortitude following a public backlash.

About 200 protesters shut down the Flinders Street Station intersection this afternoon, causing the Border Force to abandon the planned operation.

Traffic and trams were shut down for about 30 minutes as the protest went from the station steps and into the Flinders and Swanston streets intersection.

In a statement, police said that: "we understand there has been a high level of community interest and concern which has been taken into consideration when making this decision".

"Victoria Police's priority is the safety and wellbeing of the whole community and we will continue to work with our partner agencies to achieve this," it read.

Opposition Immigration and Border Protection spokesperson Richard Marles said in a statement that the handling of the operation has been "shambolic".

“This has been incredibly badly handled and Peter Dutton needs to immediately come clean on how this announcement was so botched,” said Mr Marles.

The exercise - called Operation Fortitude - had been planned for Friday night and Saturday and would have involved Australian Border Force (ABF) officers, as well as representatives from Victoria Police, Metro Trains, Yarra Trams, the Sheriff’s Office and Taxi Services Commission.

Protesters, rallied by social media, gathered outside Melbourne’s Flinders Street Station with placards reading “stop racism now” ahead of a planned press conference on Friday.

Hugh De Kretser from the Human Rights Law Centre said the proposed operation had raised concerns.

"People have a right obviously to go about their lawful business in Melbourne, and CBD without being stopped for a chat by uniform border force officials," he told SBS.

"What we've seen is a backdown from those statements which a sensible move, but the original statements are very concerning."

Related Reading Border Force will not stop people at random in Melbourne: Immigration Department

Others held signs depicting a swastika with a red line through it.

The scheduled press conference for the operation was also cancelled.

Before the cancelled conference, a Department of Immigration and Border Protection spokesperson said Border Force "does not and will not stop people at random".

"ABF officers will assist partner agencies by conducting background visa checks on individuals who are referred to us," the spokesperson said.

"... The ABF does not target of the basis of race, religion, or ethnicity."

It was in contrast to an earlier statement issued by ABF quoted Regional Commander for Victoria and Tasmania Don Smith stating that officers would be "speaking with any individual we cross paths with".

Mr Smith said that the operation was part of a "mission" to create a “secure and cohesive society”.

“You need to be aware of the conditions of your visa; if you commit visa fraud you should know it’s only a matter of time before you’re caught out," he said.

With Sacha Payne and AAP.