Authorised workers and those with COVID-19 vaccination bookings will need to show proof to board limited buses into Melbourne's CBD during a planned protest.

Melburnians heading into the city for a COVID-19 vaccination or authorised work will have to show proof to board buses and pass through roadblocks set up to thwart an anti-lockdown protest.

The Melbourne CBD will effectively be turned into a no-go zone for Saturday's planned rally, with most public transport to and from the city suspended from 8am to 2pm and road checkpoints set up.

Emergency and essential workers will still be let in, along with thousands of people scheduled to get a vaccine dose at one of the two city-based hubs.

Victoria's COVID-19 Commander Jeroen Weimar on Friday confirmed 2700 bookings at the Melbourne Convention and Exhibition Centre and Melbourne Museum will go ahead, although no further appointments are being taken.

Mr Weimar said there has not been a significant cancellation of appointments but encouraged those unable to make it to re-book.

"We'd appreciate it if you could go online or give us a call and make those changes now so we don't have staff standing around waiting for you to come forward," he told reporters.

Despite Mr Weimar suggesting there would be no alternative arrangements, the Department of Transport on Friday afternoon announced bi-hourly shuttle bus services.

The buses will run every half an hour from nine train stations where trains terminate to key drop-off points in and around the CBD.

But commuters will need to show their authorised worker permit or vaccination booking confirmation, with police officers and PSOs checking before boarding.

The same advice applies for those planning to walk, drive or grab a lift to Jeff's Shed or Melbourne Museum.

"It's the online email booking or confirmation text message. Use that and bring your ID. I'm sure the police will be sensible about it," Mr Weimar said.

The move to shut down public transport for six hours was made at the request of police after an anti-lockdown protest turned violent on August 21.

More than 4000 people attended last month's rally, which was previously described by Chief Commissioner Shane Patton as one of the most violent the city has seen in 20 years.

The police chief said intelligence suggested thousands more may be planning to attend Saturday's event as part of a worldwide series of 'freedom' rallies.

Some 2000 officers will be deployed during the police operation, which will also involve barricades and roving patrols.

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" on Saturday.