The comments dampen hopes raised by airlines that travel to and from the country could resume as early as July.
Department of Health Secretary Brendan Murphy made the prediction after being asked about the coronavirus' escalation in other nations.
Dr Murphy spearheaded Australia's early action to close its borders last March.
"I think that we'll go most of this year with still substantial border restrictions," he told the Australian Broadcasting Corporation on Monday.
"Even if we have a lot of the population vaccinated, we don't know whether that will prevent transmission of the virus," he said, adding that he believed quarantine requirements for travellers would continue "for some time".
Citizens, permanent residents and those with exemptions are allowed to enter Australia if they complete a 14-day hotel quarantine at their own expense.
Qantas - Australia's national carrier - reopened bookings earlier this month, after saying it expected international travel to "begin to restart from July 2021."
However, it added this depended on the Australian government's deciding to reopen borders.