The air safety fears come as investigators issued their final report into the fate of Malaysia Airlines flight MH17, concluding it was shot down by a Russian-made BUK missile fired from war-torn eastern Ukraine.
The Boeing 777 was downed last year, killing all 298 people on board.
The EASA stepped in as Russia intensifies its air campaign against Islamic militants in Syria. Last week Moscow launched a salvo of cruise missiles from its warships in the Caspian.
"In view of the situation in the region, Cathay Pacific suspended all flights over Iran and Caspian Sea since last Thursday until further notice," it said in a statement.
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The airline said it had received safety advisories from both the EASA and the United Nations' International Civil Aviation Organisation (ICAO) but added that neither had made specific recommendations to carriers.
Cathay already has a long-term policy not to overfly Iraq, Afghanistan, Ukraine and Syria, the statement said.
In its safety information bulletin released last week, EASA said "missiles en-route to Syria crossed airspace in Iran and Iraq below flight routes used by commercial transport aeroplanes".
Australian carrier Qantas said Wednesday that it had chosen not to suspend flights over the area.
"The Europeans said that those issues were there, but didn't make any recommendations or changes to what airlines do," said chief executive Alan Joyce.
"If there was a problem, and if it 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."
Singapore Airlines said in a statement Wednesday that it had "resumed normal routings" after previously diverting some flights to avoid the Caspian Sea area.
It did not explain why it had resumed those services.
The airline said decisions on flight routes were made "based on numerous factors" and added that it only used routes that had been cleared for use by the authorities.