A widespread community backlash has led to Victoria's chief police officer cancelling a controversial operation that would have seen people questioned about their visa credentials on Melbourne's streets.

On Friday afternoon, just hours before Operation Fortitude was set to commence in central Melbourne, Chief Commissioner Graham Ashton called off the plans for a wide-scale police initiative that was meant to target anti-social behaviour over two consecutive nights.

Operation Fortitude was first announced by the Department of Immigration on Friday morning. A press release said officers from the federal government's new Australian Border Force agency would be stationed around Melbourne's city checking "any individual we cross paths with".

The press release sparked a fierce backlash on social media and later in protests that shut down one of the city's busiest intersections, over concerns that police and Border Force officers would use racial profiling to stop and search people for possible immigration fraud.

"If you commit visa fraud you should know it's only a matter of time before you're caught out," the initial Border Force statement said.

Around the same time, Victoria Police issued a statement expressing its support for the operation, which was also set to involve transport inspectors, the Sheriff's office and the Taxi Directorate.

However, Fairfax Media understands that after Chief Commissioner Ashton learned of the "specifics" of Border Force's role in the operation, he withdrew his support, effectively aborting the entire plan.

Late on Friday afternoon, the Chief Commissioner's office issued a "please explain" to Border Force chief Roman Quaedvlieg. Commissioner Quaedvlieg conceded the press release issued by his agency was "clumsily worded" and mischaracterised the paramilitary agency's role in the operation.

The statement, largely attributed to Don Smith, Border Force's Regional Commander for Victoria and Tasmania, was widely interpreted to mean officers would stop people for random visa checks. The agency later clarified that it would check the visas of people "referred to us" by police and other agencies involved in the operation.

However, the incident has left the state government and other groups seeking an explanation from the Abbott government.

Victorian Police Minister Wade Noonan said the operation was supposed to be a standard police one, but was cancelled after the "unfortunate and inappropriate characterisation by the Australian Border Force".

Other senior members of the Andrews state government were shocked to learn of Border Force's planned role.

It is unusual for Mr Noonan or the Premier's office to receive detailed briefings on major police operations ahead of time unless it is a highly sensitive security issue.

A statement from Victoria Police said the force decided to cancel the operation after the "high level" of community interest and concern.

About 300 protesters gathered at Flinders Street Station before 2pm, the scheduled time for a press conference about the operation.

After the demonstrators blocked an intersection and security concerns grew, the press conference was cancelled.

Border Force was established in July and reflects the federal government's tougher line on national security. It combined Customs and Immigration functions into one unit. This week the agency attracted attention over the rollout of its new branding, including uniforms, which reportedly cost $10 million.

Border Force officers have more powers than former department officials, including the power to detain offenders, carry guns, and gather intelligence. They can enforce migration laws, including the power to compel a person to produce documents such as visas and tax file numbers to check whether they are an unlawful non-citizen.

Mr Quaedvlieg said Immigration Minister Peter Dutton, a former policeman, was not involved in the issuing the press release. A spokesman for Mr Dutton said "ministers don't direct operational matters". He did not respond to questions over whether he knew of the operation in advance.

Labor's immigration spokesman Richard Marles said Mr Dutton should "come out of hiding" to explain "the shambles that has seen a cross agency operation compromised and a key government agency left red-faced".

The Australian Border Force did not respond to questions posed by Fairfax Media including how much was spent on the operation.

Holy moly! The Border Force are actually TRAPPED in this building by the crowd!! pic.twitter.com/nDBUrgowlS— Liam Mannix (@liammannix) August 28, 2015

"We Are Declaring Victory Because We Shut Border Force Up" https://t.co/afEWNN1uGG— Liam Mannix (@liammannix) August 28, 2015

About 20 trams trapped. Other trams going backwards! pic.twitter.com/yD5fx8W147— Liam Mannix (@liammannix) August 28, 2015