The Chinese and Indian airlines identified have not submitted their 2011 carbon emission data to the EU yet, whereas 1,200 other carriers have already handed over their reports, said the statement.
The Chinese carriers could face fines totaling 2.4 million euros ($3.09 million), and the two Indian airlines face fines of 30,000 euros, The New York Times reported.
The EU decided to suspend its ETS in February to wait for a global market-based mechanism to cut emissions, to be discussed at the International Civil Aviation Organization's meeting in September.
However, Yan insisted that technology and operational improvements are the most effective methods of aviation emission reduction, rather than the carbon tax, and that developing countries should be assisted in achieving those.
Statistics from the CAAC show that the Chinese civil aviation industry reduced its carbon emissions by 240,000 metric tons in 2012 compared with 2011.
Yan added that the country has continued to attach huge significance to aviation emissions and has made progress through optimizing its airspace structure and other technological methods.
China Eastern Airlines Co Ltd became the first Chinese carrier on Friday to get an Airbus 320 aircraft, equipped with special wing-tip devices that cut emissions.
The devices, known as "sharklets", are placed at right angles at the end of the wing. They are made from light-weight materials that can offer up to 4 percent fuel reduction, according to Airbus.
"China Eastern will introduce 97 more sharklet-equipped A320 aircraft to our fleet," said Shu Mingjiang, its vice-president of flight operations.
Shu added that China Eastern plans to add about 200 new aircraft between 2013 and 2015, which will improve the airlines' overall fuel efficiency.
The use of advanced biofuels - a recognized safe and efficient method of reducing carbon emissions - in aviation is also becoming a major industry issue for airlines and aircraft manufacturers.
Guenther Matschnigg, senior vice-president of the International Air Transport Association, told the Beijing forum that governments should encourage the use of aviation biofuel, and that if all flights used it, carbon emissions could be cut by 80 percent.
A spokesman for Air France-KLM Group also added that biofuel is currently the industry's best alternative to helping reduce carbon emission.
He added the use of biofuel reduces the ecological footprint in the air and on the ground, and that the French carrier expects the fuel to account for 1 percent of its fuel needs by 2015.
Air China took its first test flight using biofuel in 2011, and China Eastern has also completed a test flight using a mix of fuels including used cooking oil - or gutter oil - and palm oil, in April.
However, the high price of biofuel is still a challenge to the industry, at almost six times that of conventional fuel.
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