The new screening requirement covers direct flights on Emirates, Etihad, Qatar Airways and Qantas Airways.
Australia on Friday announced it would increase screening of passenger baggage on flights from Dubai and Abu Dhabi in the United Arab Emirates, as well as Doha, Qatar.
While the directive stops short of the sweeping electronics ban introduced last month by the United States and Britain, it may include targeted screening of passengers' personal electronic devices.
Emirates and Etihad Airways, two of the largest airlines in the Middle East, said the measures would take effect on Thursday.
"The new directive requires additional screening at the gate, but there is no restriction on electronic devices," said an Emirates spokesperson.
The new screening requirement covers direct flights on Emirates, Etihad, Qatar Airways and Qantas Airways. It does not apply to flights bound for the UAE out of Australian airports.
Etihad operates two daily flights to Sydney, while Emirates has 11 daily flights to international airports across Australia.
Regional carriers have since last month scrambled to cope with the US and British bans on laptops and tablets on board direct flights out of key Middle East airports.
Airlines including Emirates and Etihad have introduced complimentary services enabling passengers to continue to use their personal electronics after check-in and until boarding.
Qatar Airways has announced it will offer free laptops for business class passengers flying to the United States.
The US ban went into effect on March 25 on nine airlines in Turkey, Morocco, Jordan, Egypt, Qatar, Saudi Arabia, Kuwait and the United Arab Emirates.
The British ban targets direct flights on all airlines out of Egypt, Turkey, Jordan, Saudi Arabia, Tunisia and Lebanon.
Officials from both countries cited security concerns for the ban, which has come under criticism as another measure targeting Muslim-majority countries.
Unlike the United States and Britain, Australian officials say there is no specific threat behind the new screening requirement.