The decision by an EU court was widely hailed by environmentalists but the Fitch ratings agency said it raised the spector of a global trade dispute.
The European Court of Justice in Luxembourg dismissed arguments that imposing the European Union's cap-and-trade carbon credits program on flights to and from European airports infringes on national sovereignty or violates international aviation treaties. U.S. and other non-European airlines had sued the EU, arguing that they were exempt from the law.
Environmentalists called the law a first step in controlling carbon emissions in a key economic sector, and EU officials said they expected airlines to comply.
But Fitch Ratings said the decision could deepen rather than quell the dispute, raised in a lawsuit brought by the trade organization Airlines for America and several U.S. airlines and supported by China, India and other countries with international carriers.
"We believe threats of trade retaliation over the EU's cap-and-trade system will pose growing threats to aviation market access in both developed and emerging markets next year," Fitch said.
Retaliation could come in the form of slot allocations at airports and authorizing routes, especially in developing countries, Fitch said.
The U.S. airlines said the regulation was tantamount to "an exorbitant tax," but the EU said the added costs would amount to a few dollars per ticket and would open the way for efficient airlines to make money rather than lose it.
The carbon trading program, due to go into effect Jan. 1, is one of the widest-reaching measures adopted by any country or regional bloc to regulate emissions of greenhouse gases blamed for climate change. It aims to make airlines accountable for their carbon emissions, which contribute to global warming.
Although only 3 percent of total human-caused carbon emissions come from aircraft, aviation is the fastest-growing source of carbon pollution.
U.S. airlines most affected are United Continental, Delta and American Airlines, all of which derive more than 20 percent of global revenues from trans-Atlantic traffic, Fitch said.
The U.S. trade group said its members would comply with the EU directive "under protest," while reviewing legal options.
"Today's court decision further isolates the EU from the rest of the world and will keep in place a unilateral scheme that is counterproductive to concerted global action on aviation and climate change," Airlines for America said in a statement from Washington. "Today's decision does not mark the end of this case."
Under the scheme, each airline will be allocated pollution permits slightly less than its average historical emissions record. If it exceeds its limit, it can buy permits from other airlines that have emitted less than allowed and have leftover permits to sell. Emissions are counted for the entire route of an aircraft that touches down in Europe.
The intention is to induce airlines to emit less carbon by upgrading their fleets or becoming more efficient.
The International Air Transport Association voiced disappointment with the ruling, saying that "unilateral, extra-territorial and market distorting initiatives" like the EU's only make it harder to reach a deal through the International Civil Aviation Organization, the U.N. regulatory agency for airlines.