Brendan Murphy downplayed the prospect of a widespread easing of border restrictions, meaning dreams of international travel this year remain on hold.
"I think the answer is probably no," Professor Murphy told the ABC on Monday.
"Even if we have a lot of the population vaccinated, we don't know whether that will prevent transmission of the virus."
Meanwhile, Australian authorities are chasing more details after Norway reported a small number of very frail people died after receiving the Pfizer vaccine.
Health Minister Greg Hunt says it may influence what advice the Therapeutic Goods Administration provides for Australia's vaccine rollout.
Mr Hunt says at this stage there is no change to Australia's planned vaccine program, which is due to start next month.
The government is planning to distribute the Pfizer vaccine as well as the locally produced AstraZeneca jab.
Nobel Prize winning immunologist Peter Doherty has no major concerns about the Pfizer vaccine.
"When you roll out enormous amounts of vaccine and vaccinate enormous numbers of people very, very quickly, some people are going to get sick and some people are going to die because they would get sick and die anyway," he told Brisbane radio 4BC.
He also backed the safety of the AstraZeneca vaccine, which he expects will save lives.
"You don't expect there to be any danger in the sort of product they're using and I don't think there's any evidence there has been," Professor Doherty said.
I'd be surprised if the vaccines don't dramatically reduce transmission.
A survey of more than 1200 people by market researcher Roy Morgan has found more than three quarters of Australians are keen to be vaccinated.
Preparations for the Australian Open tennis tournament have been thrown into disarray after five more players tested positive for coronavirus.
More than 70 players have been forced into hard lockdown in hotel quarantine, meaning they will not be able to train for two weeks.
The influx of international sports stars has also shone a light on the thousands of Australians still stranded overseas, unable to come home.
The federal government has secured 20 additional charter flights to bring more Australians home before March.
But the government is facing calls to ramp up efforts, with the global pandemic quickly becoming much worse across Europe and the United States.
NSW, Victoria and Queensland recorded no new locally acquired coronavirus cases on Monday.