Amanda McMillan, managing director of Glasgow Airport, said a rethink is required if Scots businesses are not to suffer.
Her comments came after she and her counterparts in Edinburgh and Aberdeen met Scottish Transport Minister Keith Brown to campaign for a reduction in Air Passenger Duty.
The tax is currently charged at £13 per passenger each way on a flight up to 2000 miles. It means a short haul trip from a UK airport incurs the charge and any connecting flight from London sees another charge. Chancellor George Osborne last week announced plans to increase the tax on long haul journeys.
If a couple fly from Glasgow to Paris via Heathrow and back it will cost an extra £104 in taxes.
However, flights for two, direct from Manchester or Heathrow, would cost £52.
Mr Brown said a family flying from Scotland to Lapland to see Santa would be hit with an unwanted Christmas present of £104 in taxes.
The airport bosses said the charge was pushing up the cost of tickets and putting off airlines from coming to Scotland.
Ms McMillan said: "Aviation plays a critical role in supporting the growth of the UK economy and this role is even more profound in Scotland given the country's location on the periphery of Europe.
"Travelling by air is not a luxury but an essential element of business and family life, yet we continue to have the highest levels of taxation in the EU.
"It was extremely disappointing, therefore, that despite repeated representations to the UK Government, the Chancellor in his Autumn Statement opted to further increase levels of Air Passenger Duty (APD).
"APD is already proving a significant barrier to attracting new routes and unless there is a fundamental rethink, I have no doubt Scotland's domestic and international connectivity will suffer."
Mr Brown said the Scottish Government White Paper on independence proposed a 50% reduction in the tax to help Scottish businesses.
He said: "Travellers flying to and from Scotland this Christmas should be looking forward to seeing family and friends, not worrying about the cost of this unfair tax.
"We have long argued that Scotland should have power over APD. It was recommended by the Calman Commission in 2009, but the UK Government has failed to take action.
"It is clear the current APD situation puts Scotland at a competitive disadvantage when it comes to attracting visitors and businesses from overseas.
"It is the most expensive aviation duty in Europe, adding significantly to the cost of flying to and from Scotland."