Federal Health Minister Greg Hunt said the federal government will be looking to initially use the "additional capacity" on repatriation flights to bring Australians stranded overseas home.
"We will continue to bring Australians home," he said.
On Friday, Prime Minister Scott Morrison announced that in the weekly cap on international arrivals on commercial flights into Australia.
That means the number of people allowed to enter the country each week will drop from 6,070 to 3,035 beginning on 14 July.
Mr Hunt said the Department of Foreign Affairs and Trade is assessing how many extra flights will need to be arranged by the federal government.
"There will be a decrease in commercial arrivals but an increase in what are called facilitated arrivals to Howard Springs in the Northern Territory. Some of those flights have been under-subscribed in recent weeks so there is that capacity to bring additional Australians home via Howard Springs."
He also issued a warning to commercial airlines seeking to increase ticket prices due to the cap.
"I hope that there is nobody who seeks a commercial advantage from difficult circumstances. That is a strong, clear message."
About 30,000 Australians are still overseas and trying to get home.
Australians stranded overseas have told SBS News they are .
Gene Crowe said the the cut will have "dire" consequences for him, his wife and two children as they wait to return to Australia from Singapore.
"I've got my wife and my children in tears. The people that I know that are also trying to get home, are just devastated."
Mr Hunt said he has "immense sympathy" for vulnerable Australians overseas in extenuating circumstances, and he urged them to seek assistance under the vulnerable passengers program.
"This is why for the best part of 18 months we have been ensuring that there are pathways for Australians to come home - for humanitarian reasons, to return for work.
"They have my deep, profound, immense support and sympathy because these are difficult decisions. And it is always about keeping the country safe."
Mr Hunt said the data on the incidence of COVID-19 cases in hotel quarantine showed the federal government had made the right decision in banning flights from India to Australia between 27 April and 15 May.
"We made the right decision around India. We reduced the rate of positive cases from 14 per cent to below 1 per cent," he said.
He said the federal government had struck the right balance on the international arrivals cap as there had been pressure from state leaders to cut the cap on international arrivals by as much as 80 per cent.
"We haven't closed the borders, we have reduced the flights. And as much as possible we will try to provide as many other opportunities to bring people home through the facilitated flights."
With less than six percent of the population fully vaccinated, Australia is ranked last among 38 OECD countries for the pace of its vaccine rollout, according to analysis by Our World in Data.
Minister Hunt said he was happy with the improvement in vaccination rates this week.
On Friday, there were 151,496 vaccines administered, marking a five-day total of 746,983. The week total is higher than the previous week by 49,000 doses.
The looming drop in travellers has raised concerns among industry groups of worsening skills shortages.
Australian Industry Group chief executive Innes Willox said limits on international arrivals amounted to "turning off the tap of critically needed skilled workers" and should to be removed at the earliest opportunity.
Australian Medical Association president Omar Khorshid said the caps will exacerbate the shortages of doctors and nurses as well as other critical workers in Australia.
The federal government said more than half a million Australians have returned home to Australia since March 2020.
Additional reporting: AAP
