Health authorities fear the combination of flu and COVID-19 will create a difficult winter and increase pressure on hospitals, health system and wider community.

The state's COVID-19 figures have been climbing this week with the Omicron variant BA2 becoming dominant over the original Omicron strain and with international borders reopening, influenza will make its way in to the country.

"Winter will be challenging, it always is whether you've got a pandemic or not, flu for instance, always knocks our health system around every single winter," said Premier Daniel Andrews on Thursday.

Grampians Public Health Unit clinical director Professor Rosemary Aldrich warned Omicron BA2 was more infectious than Omicron BA1.

"Omicron BA2 is 1.4 times more infectious than Omicron BA1 so while mask-wearing rules have changed we should still be wearing them to protect ourselves, particularly in confined spaces or when we cannot physically distance from others," she said.

"We are expecting that influenza will come to us in higher numbers this year, particularly now that we are welcoming international travellers into the country. In addition to this, people may be more susceptible to the flu unless they get vaccinated in a timely manner because we haven't seen as much flu in the past two years."

UFS chief executive Lynne McLennan said continuing the health and social distancing measures learned throughout the pandemic would help reduce the risk, but vaccination was the key.

"The absolute best way to reduce the risk of infection and help protect our over-worked health system is to make sure you are vaccinated against both COVID and influenza," Ms McLennan said.

"Due to Australia's borders now being open, the Department of Health is expecting there will be high levels of influenza virus circulating this winter. Therefore it's more important than ever to be protected prior to the flu season this year."

Flu infections typically peak in August but with little to no flu circulating in the community over the past two years because of lockdowns and strict health precautions, authorities cannot predict when flu infections might peak this year.

Ms McLennan said flu vaccinations were recommended from mid-April onwards to ensure protection before the peak of the flu season, and she called on those who have not yet had their COVID-19 booster vaccination to get jabbed.

"If you haven't had your booster yet, we recommend doing this as soon as possible," she said.

Pharmacists are also recommending wearing of KN95 masks to give higher levels of protection against both viruses, and urged anyone with symptoms to get tested and isolate.

"The fact that the new COVID variants are circulating at alarming numbers, with increases in positive cases in Victoria, means there is no room for complacency," Ms McLennan said.

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"Please be COVID-safe as you move around the community. Masks are optional in many settings, however consider whether you want to wear one anyway if appropriate social distancing is not possible."

Professor Aldrich said those at higher risk of flu include children aged six months to five years, who are also not vaccinated against COVID-19, people who are immune compromised and people aged over 65.

Federal health minister Greg Hunt last week announced a further $2.1 billion in "winter preparedness" funding for states and territories to plan for COVID and flu.

The cash injection will support vaccines, vulnerable populations and extra support for aged care.

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