The growth in aviation has added to pollution fears
The European Parliament has backed a law to include aviation in Europe's CO2 Emissions Trading Scheme (ETS) for cutting greenhouse gases.
MEPs voted 640 to 30 for aviation to be included in the scheme from 2012. It includes both EU and non-EU airlines.
Under the UN's Kyoto Protocol, the EU is required to cut its CO2 emissions by 8% from 1990 levels by 2012.
Airlines will have to cut emissions by 3% in the first year, compared to 2005, and by 5% from 2013 onwards.
The measures will now be ratified by the 27 EU member states, which agreed the deal in June.
Industries included in the ETS have to buy and sell permits that allow them to emit carbon dioxide into the atmosphere.
Airlines will have to pay for permits covering 15% of their pollution quotas, the remainder being issued free.
Aviation currently only accounts for about 3% of the EU's total greenhouse gas emissions, but the sector has seen an 87% increase in CO2 since 1990.
The new legislation says the revenues generated from the auctioning of emissions permits should be used to fund: measures to combat climate change, research on clean aircraft, anti-deforestation measures in developing countries and low-emission transport. Within that framework, the member states will decide how to allocate the revenues.
US officials and US-based airlines have criticised the extension of the ETS to aviation, arguing that the EU has no right to force airlines using its airspace to abide by the ETS rules. They say the EU must wait for a global agreement to be reached.
Peter Liese, a German MEP who helped negotiate the aviation package, said that "of course, a global agreement is our final goal, but the inclusion of third country flights starting and landing in Europe is a major step for the global fight against climate change".
"Other industries like steel would very much like to be in such a situation," he added.
The ETS began operating in 2005. It applies to major energy and industrial concerns which collectively account for about 40% of the EU's total greenhouse gas emissions.
The aviation deal backed by the MEPs excludes: light planes with a take-off weight under 5.7 tons, UN-approved humanitarian flights, firefighting or other emergency flights, flights by police, customs or military forces, research flights and flights by small, low-emission airlines.
The deal was criticised by the German carrier Lufthansa on Tuesday. A spokesman quoted by Reuters news agency said the ETS was "ecologically counter-productive and economically harmful".
The aviation scheme will include official flights by EU heads of state and ministers.
The European Commission reckons that the scheme could increase return air ticket prices by 4.6 to 39.6 euros (£3.6 to £31) by 2020, depending on the journey length.