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"We've received letters from at least the French and German governments," one official told EurActiv.
"It's been known since the measure was adopted that this was controversial. Now we're nearing the 1 January deadline, it's clear that there is some nervousness."
From the start of next year, the EU plans to make all airlines using European airports pay for their carbon pollution under the Emissions Trading Scheme (ETS).
But Chinese threats of trade retaliation against European airlines - and French plane-maker Airbus - have spooked the aviation industry and politicians alike.
EurActiv understands that in mid-May, German Transport Minister Peter Ramsauer wrote to the EU's transport commissioner, Siim Kallas, warning that foreign airlines should only be subject to the ETS if it caused no harm to European airlines.
"Mr Ramsauer is having some worries on the inclusion of air traffic in the ETS and he asked Mr Kallas to present proposals on how to counter the unwillingness of third [party] states to involve their airlines in it," a diplomat told EurActiv.
"There might be signals that some third-party states can actually prevent such an inclusion of the airlines," he added. "This would, of course, not meet our expectations of 'competitive neutrality'."
Germany's position still being shaped up
EurActiv understands that Mr Ramsauer was writing in a personal capacity and might yet face opposition from other government departments in Berlin, such as the environment ministry.
But 'competitive neutrality' or a 'level playing field' is a key concept in Germany's Basic Law and its invocation could prove serious enough for a challenge to the ETS legislation.
"Whether we would support a change or modification is a major question that could only be answered when the time comes," the diplomat said. "There is a sensitivity to the problem."
Isaac Valero, spokesperson for Climate Action Commissioner Connie Hedegaard, urged EU governments to stand firm on the 'polluter pays' principle.
"There is no chance that we are backing down from already approved legislation," he told EurActiv.
Valero acknowledged that the Commission had also received a letter from the French government, but insisted that Europe remained united.
"France is not stepping down from the legislation, just raising Airbus's concerns and flagging how we can address the issue," he said.
Commission officials privately seem surprised by the reaction from France and Germany, but say they were prepared for external pressure over extending the carbon market to aviation.
On 5 June, Tom Enders, the chief executive of Airbus, sent a letter to Climate Action Commissioner Hedegaard, warning that it would be "madness to risk retaliation" from countries such as China by including their planes within the EU's cap and trade system.
"The Chinese have put some robust threats to Airbus but you cannot budge to this kind of blackmail," an EU source told EurActiv. "We are going to have to fight this fight."
The EU directive setting up the ETS already allocates 85% of emissions allowances to aircraft carriers for free, as a strongly-worded reply from Commissioner Hedegaard to Enders's Airbus letter, seen by EurActiv, reiterates.
"If nations and regions do not defend their legitimate right to legislate," Hedegaard says, "it would send an extremely unfortunate signal and create problems not just for the global climate but also for European companies and businesses".
Signed by Commissioner Hedegaard, the letter was also approved by Transport Commissioner Kallas and Trade Commissioner Karel de Gucht, and it was supported by Commission President José Manuel Barroso, Valero said.
Commission officials believe that if Brussels backs down on the third and most critical phase of the ETS, its flagship policy will lose momentum, and it will lose international respect.
This resolve may be tested in court. On 6 June, the China Air Transport Association (CATA) said that it would back legal action to prevent the ETS from being applied to the 16 Chinese airlines which have the right to operate between China and Europe.
A legal challenge by a US air industry group is also due to be heard by the EU Court of Justice on 5 July.