"If properly designed, it can play an important role in tackling aviation’s contribution to global warming along with investment in technology and more efficient infrastructure," he added.
One concern recently voiced by airlines appeared to have been taken into account in the scheme announced in Brussels on Wednesday.
IATA said the EU would allow carriers to trade emissions with other sectors of industry, instead of segregating airlines from the other players in emissions trading.
Bisignani said the Commission had to deal with two other major issues — the EU’s fragmented air traffic control and fears that its emissions rules might be different from those set elsewhere in the world.
A single European sky could reduce carbon dioxide emissions by 12 percent, he added.
"We have 34 air traffic control centres in Europe but only one in the USA for a similar traffic and land size. This leads to inefficiencies, delays, and too much time in the air," Bisignani said.
IATA also called on the EU to follow guidelines on emissions trading being drawn up by the International Civil Aviation Organisation (ICAO) next year. "We must have a global approach for a global problem," Bisignani said, underlining that IATA would work with EU Transport Commissioner Jacques Barrot to "improve the design of the package".