New pandemic orders which kick in at 11.59pm on Wednesday will demand workers in key sectors - including health and aged care, disability, emergency services and food distribution - get their third dose to continue working.
Those eligible for a third dose on or before Wednesday will be given until Saturday, February 12 to get their booster, with workers not yet eligible told to get it within three months and two weeks of their deadline.
This means residential aged care workers have until March 1, health care until March 29, and emergency, disability, quarantine, corrections and food distribution workers must get their third dose by March 12.
Food distribution workers include manufacturing, warehouse and transport workers but not retail supermarket staff.
Workers with a valid medical exemption are also not included in the mandate.
It comes as the vaccine rollout for children aged between five and 11 has been marred by supply issues on the first day of the program.
Royal Australian College of General Practitioners Victorian chair Anita Munoz said supply was coming in "sporadically" with some GP practices given 100 doses a week and others given 100 doses a fortnight.
"That is, really, terribly inadequate numbers for general practices to vaccinate kids," she told AAP.
"The supply itself is unreliable and sporadic, and we understand that's in part because the logistics industry is affected by COVID itself.
"But it's not just that, when supplies finally do arrive they're coming in in inadequate numbers."
She said the RACGP had given "a lot of feedback" to the federal government about how to ensure the latest vaccine rollout would run smoothly and efficiently.
"What we really wanted to avoid was repeating any of the mistakes we needed to learn from last year," she said.
"I am disappointed that these kinds of issues are being repeated."
While some GP clinics are standing down practitioners and other staff due to COVID-19-related isolation requirements, she said this was not affecting the rollout as much as supply issues.
The head of Australia's vaccine rollout, Lieutenant General John Frewen, denied there were supply problems and on Monday encouraged parents to book through pharmacies and state hubs if they cannot get in with a doctor.
Victoria has doubled the number of state-run vaccination sites available for children aged five to 11, with 36 sites around the state.
COVID-19 Commander Jeroen Weimar on Sunday said state clinics had enough supply and the health department was working closely with GPs and pharmacies.
Victoria recorded 34,808 new COVID-19 cases and two people died from the virus, the health department said on Monday.
The new infections included 17,190 from rapid antigen tests and 17,618 from PCR tests, with the state now managing 161,065 active cases.
There are 818 patients in hospital, 66 more than the previous day, including 118 in ICU and 28 requiring ventilators.
About 17 per cent of Victorians aged over 18 have received their third dose of a vaccine, while 93 per cent of those aged over 12 are double-dose vaccinated.
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