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"These flights will fly from priority areas from around the world, making sure that the Department of Foreign Affairs and Trade off of their intelligence and knowledge of where Australians most need assistance, target those flights," he said.

The passengers will be in addition to the caps on commercial flight passengers.

The additional arrivals will be directed to the Howard Springs quarantine facility in the Northern Territory, Canberra and Tasmania and would happen according to strict protocols to keep Australia safe.

Senator Birmingham defended the severe restrictions on international arrivals put in place since last year, saying the measures had helped Australia contain the spread of COVID-19.

With nearly 40,000 Australians stuck overseas nearly a year after the pandemic started, Senator Birmingham acknowledged people's frustrations but said the travel restrictions had been an "essential" part of Australia's COVID-19 success.

"The very first steps taken almost exactly 12 months ago to start closing Australia's borders, to put in place restrictions to keep Australians safe have worked and have been a triumph for Australia relative to so much of the rest of the world," he said.

"Australians are enjoying relative freedoms, relative openness and, of course, health successes that are the envy of the rest of the world."

Labor has criticised the federal government's approach to hotel quarantine, with opposition foreign affairs spokeswoman Penny Wong saying "Scott Morrison has refused to take responsibility for quarantine" and urging the government to establish a national system.

Responding to the criticism, Senator Birmingham questioned where the quarantine facilities would be established and where the "magical workforce" would be found.

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He said the federal government had supported state governments' hotel quarantine systems with Defence Force personnel.

He also noted that some of the Australians registering their desire to come home had done so in recent months, not in the early stages of the pandemic.

After Emirates suspended its flights to Sydney, Melbourne and Brisbane, Senator Birmingham noted other carriers were still servicing Australia and they could fill the capacity available under international arrival caps. Senator Birmingham said the repatriation flights facilitated by the government would be done in a safe way to keep Australia safe and open.

The United Arab Emirates carrier was conducting daily flights between Dubai and Sydney and Melbourne and five flights a week to Brisbane, meaning the decision will wipe out 19 flights per week for Australians in Europe and the Middle East who have been waiting months to get home.

The airline only flies Airbus A380s and Boeing 777s – two of the largest modern planes in the industry.

Responding to the decision by Emirates to suspend flights to and from Sydney, Melbourne and Brisbane, Senator Birmingham said it was a commercial decision by the airline and the places under the arrivals cap would be available to other carriers.

Qatar Airways, Etihad Airways, Singapore Airlines and Japan Airlines are still running flights to Australia for people in Europe but the cap reduction has already led to some cancellations and delays.