In last week's safety bulletin, EASA said "missiles en-route to Syria crossed airspace in Iran and Iraq below flight routes used by commercial transport aeroplanes".
Russia last week launched missiles from the Caspian Sea directed at targets in Syria, it said.
“Before reaching Syria, such missiles are necessarily crossing the airspace above Caspian Sea, Iran and Iraq, below flight routes which are used by commercial transport aeroplanes,’’ EASA said.
Howver the agency do dnot make any recommendation, adding that the advisory was to "create awareness" for airspace users.
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Cathay Pacific said it had stopped flights in response to safety advisories from both the EASA and the United Nations' International Civil Aviation Organisation.
"In view of the situation in the region, Cathay Pacific suspended all flights over Iran and Caspian Sea since last Thursday until further notice," Cathay Pacific said in a statement.
Cathay said the airline already has a long-term policy not to overfly a number of war-torn countries in the Middle East including Iraq, Afghanistan, Ukraine and Syria.
Malaysia Airlines and Air France have also reportedly made changes to their flights, the Australian reports.
Australian airline Qantas said it would not be changing flight paths.
Qantas flies over Iran on its Dubai to London leg. Qantas flies over Iran at a cruising altitutde of 39,000 feet.
Meanwhile, the Russian cruise missiles launched at Islamic State positions in Syria travel at 50 to 150 metres above the ground, but have been reported to travel 1500 kilometres through Iraqi airspace.
“If we believed any airspace had risks that were unacceptable and meant that it wasn’t safe to fly through, Qantas would not be flying through them," Qantas chief executive Alan Joyce told the National Press.
"The Europeans said that those issues were there, but didn't make any recommendations or changes to what airlines do.
"If there was a problem, and if does turn into being a problem, Qantas will not be flying aircraft through that airspace. But the information that we have is it is safe to do so."
The air safety fears come as Dutch investigators on Tuesday issued their final report into the fate of Malaysia Airlines MH17, finding that it was shot down by a Russian-made BUK missile.
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The Boeing 777 was shot down over eastern Ukraine last year, killing all 298 people onboard, including 38 Australian residents and citizens.
Dutch Safety Board chairman Tjibbe Joustra condemned Ukraine for not closing the airspace over the conflict zone.
