The first flight to Australia from Abu Dhabi landed in Sydney on Friday morning with only about a third of its seats filled, those on board say.
It comes as Prime Minister Anthony Albanese confirmed three Australian defence members were on board a US nuclear submarine that sunk an Iranian ship.
Julie Pearce was on Etihad EY450, which arrived at Sydney Airport on Friday, and questioned whether the Australian government was working with airlines to fill the few planes leaving.
"That flight was only a third full," Ms Pearce said.
She was only able to get on the 300-seat Boeing Dreamliner through her daughter, who used to work for the Emirati airline and had a connection who could get her a seat.
"They could have got a lot of people on there this morning and they didn't."
Fellow passenger Trudy Schipelliti also questioned the government's efforts to fill the planes.
"It was pretty disgusting, because there are a lot of people waiting to get out," she said.
"Most people had three seats to themselves each."
Foreign Minister Penny Wong said she was disappointed at reports flights were arriving with hundreds of empty seats.
"We are seeking to work even more closely with the airlines to try and coordinate that," she told reporters on Friday.
"We want every seat filled."
Another two Emirates flights from Dubai landed in Australia overnight and several more are scheduled to depart from the war-torn region, as passengers are encouraged to keep their tickets and stay in constant contact with their airlines.
One plane arrived in Sydney on Thursday night and another in Melbourne on Friday morning, bringing home more than 440 Australians.
Emirates is expected to operate another four flights from Dubai in the next 24 hours.
Etihad and Qatar Airways have tentatively scheduled a small number of flights, pending airspace closures.
The federal opposition has called for government-commissioned repatriation flights for stranded Australians.
Military planes were used at short notice to evacuate Australians from Israel in 2025, New Caledonia in 2024 and Afghanistan in 2021, opposition foreign affairs spokesman Ted O'Brien said.
But Home Affairs Minister Tony Burke said regular commercial flights were the best option.
"When you've got more than 100,000 people in the region who have been stranded, a charter flight option isn't going to scratch the surface on that," he said.
There are 24,000 Australians in the UAE, made up of travellers and residents, while about 115,000 are across the broader Middle East.
The federal government has deployed military assets to assist stranded Australian citizens and permanent residents.
A Royal Australian Air Force C17A Globemaster heavy transport aircraft and KC-30A multi-role tanker transport have been deployed as a precautionary measure.
The evacuations come as the prime minister confirmed Australians were on board a US submarine that torpedoed an Iranian frigate near Sri Lanka, killing 87 on board.
"We wouldn't normally confirm such an issue, but ... I can confirm that there were three Australian persons on board that vessel," Mr Albanese told Sky News on Friday.
"I can confirm also, though, that no Australian personnel have participated in any offensive action against Iran."
The Australian defence personnel were on board the submarine as part of a training rotation for the AUKUS security pact, which will provide Australia with nuclear vessels.
The submarine not only destroyed the Iranian frigate Dena but left the survivors to drown at sea in breach of international law, Greens Senator David Shoebridge said.
"This makes Australia obviously, clearly, unambiguously part of an illegal war, part of a war that is breaking down the norms of international law and making the world a less safe place," he said.
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