Prime Minister Anthony Albanese told parliament on Thursday a plane transporting more than 200 Australians was on its way to Sydney, the second to leave the United Arab Emirates city since Iran retaliated against US-Israeli strikes.
He hoped another two flights from Dubai, which were scheduled to leave on the same day, would go ahead.
"We know that there are many Australians who are waiting for an opportunity to get home," Mr Albanese said.
"The Australian government, the UAE and airlines in the Gulf states are working hard to secure more flights to get Australians home as soon as possible."
The United Arab Emirates and nearby Qatar act as major aviation hubs for Australians travelling to the region and on to other destinations such as Europe.
Qatar Airways, which partners with Virgin Australia, said all its flights remained suspended until local authorities announced the skies were safe.
The Doha-based airline said it would release an update on Friday.
Etihad Airways has suspended all flights to and from Abu Dhabi until Friday morning, local time.
The first Australia-bound flight from the UAE landed on Wednesday evening, reuniting anxious families at Sydney airport.
Mr Albanese said the situation in the region remained "dangerous and fast-moving".
There are 24,000 Australians in the UAE, made up of travellers and residents, while about 115,000 are across the broader Middle East.
Six crisis response teams are on their way to the region to provide extra consular support in response to "unprecedented" demand.
Australian Travel Industry Association chief executive Dean Long warned all travellers not to cancel their flights and instead stay in close contact with their airlines and travel agents.
People are entitled to a full refund when an airline cancels a flight.
"The worst single thing you can do is to cancel as it will reduce the number of rights you have available to you," he said.
Airlines were adding additional flights and alternative routes to Europe remained an option for people with existing travel plans, Mr Long said.
Landing on Australian soil on the first plane from Dubai, Iman Krayem was surrounded by her son Youssef and husband Nazih after leaving to see her sick father in Lebanon.
She was stuck in the UAE for several nights when Iranian missiles struck the gilded city in response to a barrage of US and Israeli attacks.
"I was crying non-stop," she told AAP minutes after clearing customs.
"It was so stressful, I didn't have my luggage, I had no clothes but I am happy to be back home now."
Among the more than 200 passengers who arrived were a group of high school students travelling to Istanbul for a robotics competition.
Charity worker Hawra Khalil, another arrival on the same plane, was in Lebanon on a humanitarian trip feeding war-torn children in several cities.
Heeding the Australian government's travel warning, Ms Khalil managed to catch a flight to Dubai, where she was grounded with a colleague.
"I just got a glimpse of it in Dubai and I had seen what people in Lebanon go through on a daily basis tenfold," she told AAP.
Iran has launched hundreds of drones in recent days across several countries including Kuwait, Qatar and Saudi Arabia in retaliation for US and Israeli strikes.
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