The partial public transport shutdown was made at the request of police after 4,000 people attended a violent anti-lockdown protest on August 21.
Some 2,000 officers will be deployed during Saturday's operation, which will involve road checkpoints, barricades and roving patrols.
Chief Commissioner Shane Patton previously labelled it the biggest Victoria Police operation since the 2000 World Economic Forum was held in Melbourne.
Organisers have flagged the protest will be moved, with a new location set to be revealed on Saturday morning.
A Victoria Police spokesman would not confirm to AAP if they were aware of the potential location change, but said the force would have a "highly visible presence".
NSW Police launched a similar operation in Sydney with CBD traffic restricted and police officers deployed in large numbers.
Minister for Police and Emergency Services David Elliott urged protesters to reconsider taking part in any demonstrations.
“There is no doubt that these protests are a risk to public health – for the community, for police as well as for the individual health of the protesters themselves,” Mr Elliott said.
“We’ve seen past protesters end up contracting COVID-19, so anyone who is still considering protesting needs take a good hard look at themselves.”
NSW Police Deputy Commissioner Mal Lanyon said officers would not hesitate to make arrests or issue fines.
"Engaging in an unauthorised protest does not comply with the public health order and anyone choosing to attend or participate for that purpose should expect to be met by the police and face penalties ranging from a fine to being arrested."