China, India, Russia and 26 other governments that oppose the charges issued a joint declaration in February that cited possible retaliatory steps such as imposing charges on European airlines.
"The last thing that we want as an industry is a trade war," said Paul Steele, director of environmental issues for the International Air Transport Association, at an industry conference in Beijing.
"The problem is that the way things stand right now, I think we are on the brink of something like that happening," he said.
The European Trading System requires airlines that fly to and from Europe to buy permits for all the carbon they emit en route. The charges took effect Jan. 1 but airlines will not be required to pay until next year.
China and India have prohibited their airlines from co-operating and Beijing has blocked purchases of European aircraft by its carriers in protest. European courts have rejected legal challenges by U.S. airlines, supported by governments including China and India.
Talks on a global system to regulate airline emissions have begun in the International Civil Aviation Organization, a U.N. body. The European Union has said it would be willing to reconsider its system if an agreement is reached.
"We're calling on all parties to get back around the table in ICAO and hammer out a solution," Steele said.
Aviation accounts for 3 per cent of total carbon emissions but is the fastest-growing source.
EU officials have defended the charges as in line with Europe's efforts to be a leader in curbing climate change. Environmentalists welcomed the program, one of the most far-reaching measures adopted by any government to regulate greenhouse gas emissions.
Other governments object that Europe should not be imposing charges on what airlines do outside Europe.
The conflict adds to uncertainty for an aviation industry that is being squeezed by high fuel prices and a weak global economy.
"We can't afford to be caught in the middle of a trade war over the EU's extraterritorial application of its emissions trading system," said the IATA's executive director, Tony Tyler.