The security measures are similar to what the US and UK recently introduced, but does not bar passengers from taking electronic devices on board.
Australia will conduct additional security checks on passengers flying directly from Muslim-majority countries in the Middle East to prevent security threats.
The increased security measures will affect passengers flying direct to Australia from Doha, Abu Dhabi and Dubai.
The new rules follow similar measures introduced by Britain and the United States, but do not include the same bans on electronic devices in the cabins of passenger flights.
"In response to national security advice, the Federal Government has made precautionary changes and instructed airlines to implement new protocols from next week," Australian Transport Minister Darren Chester said in a statement on Friday.
"Explosive detection screening will be conducted for randomly selected passengers and their baggage. Checks may also include targeted screening of electronic devices."
Affected airlines are Qantas and Gulf carriers Etihad, Emirates and Qatar Airways.
The extra security checks on passengers from the Middle East is reminiscent of the unnecessary delays and humiliation Muslims faced at airports in the US and Europe after the 9/11 attacks.