While describing the proposal as a "positive and innovative step," European airline associations said that it could cost them over 45 billion euros (60 billion dollars) from 2011 to 2022 to meet the quotas.
Under a proposal from the European Commission in December, airlines would have to meet quotas either by reducing their emissions or buying carbon dioxide credits from other industries.
But six European airline associations said in a joint statement that "the European Commission's proposal in its present form will jeopardise the long-term viability of the European aviation industry."
A study commissioned by the airlines concluded that far less of the cost could be passed on to consumers than assumed, price hikes could discourage air travel, and European carriers would struggle to compete with rivals from elsewhere.
On top of that, airlines would have to spend over 45 billion euros between 2011 and 2022 buying up credits from more fuel-efficient industries to meet their quotas.
As a result, the measures could reduce the profits of European airlines by 40 billion euros over the period, "weakening the financial stability of a number of operators," the airlines said.
EU planes account for about half the industry's carbon dioxide emissions worldwide.
Aircraft carbon dioxide emissions account for only about three percent of the global total but they have increased by 87 percent since 1990, according to the Commission, the EU's executive body.
Their real impact on global warming is amplified two to four times because planes flying at high altitude leave condensation trails which add to the greenhouse gas effect.
Under the Commission's proposal, which still has to be adopted by EU member states and the European Parliament, airlines would be subject to emissions quotas from 2011 on intra-European flights and from 2012 for flights originating outside the bloc.
It would cover both EU and foreign aircraft operators and the quotas would be based on emission levels from last year.
Washington has raised the prospect of launching legal action against the measures if Europe goes ahead with them.