Airlines from China, Russia, the US and Latin America say that the cost of participating in ETS for aviation - passed on to passengers - will be unreasonably high for fast-growing operators, giving them a competitive disadvantage compared to European airlines.
They question whether the scheme complies with existing bilateral agreements on open skies or with WTO rules, threaten to take legal action, and ask to be exempted.
But why should "a student flying from Scotland to Germany pay a CO2 emission fee while a Chinese businessman flying from Beijing to Europe does not?", asks Connie Hedegaard, the EU's environment commissioner.
As from 1 January 2012 the EU ETS for aviation will apply to all flights arriving or departing from an EU airport, covering all operators regardless of whether they are based in the EU. It is the first step towards the final goal, a global sectoral agreement covering all greenhouse gas emissions from aviation.
Possible exemptions
Under the ETS directive, incoming flights to Europe with airlines from third countries may be exempted from the scheme if those airlines take "equivalent measures" of their own to reduce CO2 emission.
To benefit from this provision, China and other third countries must show the EU that they have "equivalent measures" in place. Ultimately it is up to the Council - thus, to member states - to decide whether or not they accept.