Speaking before a Senate estimates hearing on Wednesday, Professor Paul Kelly said the country was well placed to handle any new variants that may emerge in coming months.
"While there may be challenges ahead, I see no reason why, even with the easing of restrictions, the strong position in Australia will not likely change over the winter months," he said.
"The 2022 winter season may well present challenges to health systems, health care providers, aged care and disability care residents, communities and the economy."
Health officials have warned the coming winter could bring with it a spike in cases combined with the first flu season in the country since the start of the pandemic.
While Prof Kelly said the threat of a new variant was a possibility, Australia would be prepared to handle the situation.
"Work is well under way in all states and territories ... to prepare our healthcare system for the likely co-circulation of COVID-19 and influenza," he said.
"The general principle will be to move away from reducing COVID-19 transmission to protecting people at higher risk of developing severe disease, essentially reducing harm."
Prof Kelly stressed vaccine booster take-up was essential in minimising the number of hospitalisations and deaths from the virus.
It comes as a second booster rollout began earlier this week for older and vulnerable Australians ahead of the coming winter.
Latest vaccination figures show more than 94 per cent of those in aged care - and more than 90 per cent of those over 70 - have had their first booster.
The head of the country's vaccination rollout, Lieutenant-General John Frewen, said Australia was ranked 22nd out of OECD countries for the booster rollout.
He told estimates the rate was due to the booster rollout starting later than other countries and other nations using different metrics for the rollout.
Australia's OECD ranking for two doses is fifth.
"Originally we were much lower down the OECD rankings for two doses, and as our rollout has proceeded, we've climbed right to the heights," Lt Gen Frewen said.
"We will see that through the booster program as well."
The rollout head also attributed the slower take-up rate for boosters due to many people having contracted the virus and not being as fearful of the newer variants, along with complacency.