The strict limit on the number of inbound passengers per flight allowed to Australia has forced Qatar Airways to stop accepting new bookings.
Qatar Air said hundreds of people a day are told they cannot be accommodated on their booked flight.
Through late October the airline can now only carry a maximum of about 4,500 passengers.
It says it has repatriated 180,000 Australians since the start of the pandemic.
"Due to the dynamic nature of the pandemic, airlines operating flights to Australia have faced ever-changing restrictions, often imposed on short notice," Qatar Airways said.
"These combined restrictions have resulted in many passengers having their tickets rebooked onto later flights several times as demand exceeds the new caps announced."
The Board of Airline Representatives of Australia industry group estimates there are still 100,000 Aussies stranded overseas trying to return.
Under the current passenger cap it could take six months to get them home, BARA says.
Sydney Airport only permits 350 passenger arrivals per day and Brisbane and Adelaide only allow 500 passengers per week.
This has led to a huge spike in airfares with Qatar Air admitting it has been prioritising premium passengers to make the flights economically viable.
