Protesters flooded a Melbourne railway station earlier to protest the announcement of the controversial operation.
The Department said the weekend launch of inter-agency Operation Fortitude would target "everything from anti-social behavior to outstanding warrants." The operation was intended to combine ABF with transport and other enforcement agencies.
Victoria Police said in a statement published on its social media it has "made a decision not go ahead with this weekend’s Operation Fortitude."
In the clarifying statement, it said the ABF will continue to "assist other agencies in this operation by conducting background visa checks on individuals who are referred to us by Victoria Police and other agencies."
The ABF is a new outfit composed of immigration and customs offices.