In a message on Eurocontrol's website, the European Aviation Safety Agency (EASA) wrote: "Due to the possible launch of air strikes into Syria with air-to-ground and/or cruise missiles within the next 72 hours, and the possibility of intermittent disruption of radio navigation equipment, due consideration needs to be taken."
The potential threat to carriers has grown on a day of rising tensions and threats as the US, Britain and France seek to co-ordinate their response to last week's suspected chemical attack which killed 70 people in the rebel-held town of Douma.
The sabre-rattling began when Alexander Zasypkin, the Russian ambassador in Beirut said: "If there is a strike by the Americans, then...the missiles will be downed and even the sources from which the missiles were fired".
His remarks, raising the possibility of a US-Russian confrontation, provoked a belligerent response from President Donald Trump, who tweeted: "Russia vows to shoot down any and all missiles fired at Syria.
"Get ready Russia, because they will be coming, nice and new and "smart!" You shouldn't be partners with a Gas Killing Animal who kills his people and enjoys it!"
He added: "Our relationship with Russia is worse now than it has ever been, and that includes the Cold War. There is no reason for this.
"Russia needs us to help with their economy, something that would be very easy to do, and we need all nations to work together.Stop the arms race?"
Earlier, a Kremlin spokesman said Russia wanted all parties to "avoid any steps that are not provoked by anything and could significantly destabilise an already fragile situation in the region."
Prime Minister Theresa May held separate phone calls with French President Emmanuel Macron and Mr Trump on Tuesday and all three agreed the international community "needed to respond to uphold the worldwide prohibition on the use of chemical weapons", calling the apparent attack on Douma "utterly reprehensible".
But some MPs are calling for a vote in Parliament before any military operations are launched.
Conservative MP John Baron told the Today programme: "If there is going to be significant military intervention then I think Parliament has every right to ask questions particularly given our poor track record on previous interventions across the region."
Mr Macron said on Tuesday that any operations would target the Syrian government's chemical facilities, rather than the Assad regime's allies or any person in particular.
He called for a "strong and joint response" to the attack on Douma on Saturday and said France, the US and Britain will decide how to respond in the coming days.
On Monday, the US President promised a decision on Washington's response to the attack "within 48 hours".