Fast-growing Gulf airlines Emirates
Tim Clark, the president of Emirates, Dubai's flag carrier and the world's largest long-haul airline, told the Gulf News newspaper that the company would spend over 40 million euros (33 million pounds) in 2012 to purchase additional emission allowances.
Unfortunately, while we always try to make our fares as competitive as possible, the additional costs of the EU Emissions Trading System programme will almost certainly have to be passed on to customers, but how this will be done has not yet been determined, he said.
Under plans to tackle climate change that came into effect on January 1, airlines touching down or taking off in the 27-nation European Union and three neighbouring nations must account for their CO2 emissions as part of an expansion of the world's largest carbon market.
Abu Dhabi's Etihad Airways echoed Emirates' views.
Etihad will end up bearing an extra cost of 310 million euros over the next nine years, Linden Coppell, Etihad's head of environment told the paper.
It is inevitable that such a cost would have an impact on fare levels. This is why we want to ensure we have a fair global system, Coppell said.
No immediate comment was available from either Emirates or Etihad.
The statements from the Gulf airlines come close on the heels of German carrier Lufthansa warning on Monday of higher ticket prices.
The EU says the new scheme, which already applies to other industries, is the fairest way to cope with aviation's contribution to global warming.
However, it has sparked a trade spat, with the United States, China, India and others accusing it of infringing their sovereignty.
(Reporting by Praveen Menon; Editing by Sitaraman Shankar)