The court’s decision comes amid increasing pressure from some of the biggest trading partners of the 27-member bloc to suspend or amend application of the legislation to expressly exclude non-European Union countries — at least initially. Failing that, several governments have vowed to take their own legal action or retaliate with countervailing trade measures.

Although airlines for now will receive most of the permits they will need free, the European Union estimates that ticket prices could rise by as much as 12 euros ($15.65) on some long-haul flights to cover the cost of the additional permits required.

Airlines for America, an industry lobby group and one of the plaintiffs in the case, said that its members would be required to pay more than $3.1 billion to the European Union from 2012 to 2020. It said its members would comply with the system under protest but would also review options for pursuing the case in Britain’s High Court, which had referred the original complaint to the European court in 2009.

“The court did not fully address legal issues raised and has established a damaging and questionable precedent,” the airline group said in a statement.

In a letter dated Dec. 16, Hillary Clinton, the United States secretary of state, and Ray LaHood, the secretary of transportation, said Washington would be “compelled to take appropriate action” if Brussels proceeded, though the letter did not specify what form that might take.