The announcement comes just a week after the national cabinet decided to reduce the cap on international arrivals by 50 percent until mid-February.
The federal government says it has so far helped to arrange 90 flights to bring 446-thousand Australians home.
Dubai-based airline Emirates has also unexpectedly suspended all flights to Australia's east coast due to what it says are operational reasons.
For Yasir Muhmood and his wife, who are stuck in Pakistan, the cancellation of Emirates flights means there's only one airline flying from there to Australia.
The federal government has not outlined which exact countries will be included in the repatriation flights.
Acting Foreign Minister Simon Birmingham says it is being decided on the basis of the most need.
These flights will fly from priority areas around the world, making sure the Department of Foreign Affairs and Trade offer their intelligence and knowledge of where Australians most need assistance, target those flights. Of crucial importance, these facilitated flights will bring Australians home over and above the caps that have been agreed [to] by National Cabinet. So it will create additional places for Australians to get home, over and above those caps.
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