The plans include fines for member states that fail to meet targets for the creation of a "Single European Sky", a scheme that Brussels says will cut costs, reduce pollution and increase safety.
Unions say the plans will lead to job losses and affect work conditions while France -- where hundreds of flights were cancelled due to the strike today -- and Germany expressed doubts.
But EU Transport Commissioner Siim Kallas, revealing the details of the plan at the European Parliament, said the "ambitious reforms" would reduce congestion in European airspace.
"If we leave things as we are we will be confronted with heavy congestion and chaos in our airspace," he added.
The proposals by the European Commission -- the EU's executive arm -- must be approved by all 27 member states and the European Parliament before becoming law.
Brussels said it would have greater powers to set air traffic control performance targets for member states "and enable sanctions to be applied when targets are not met."
The Commission laid the blame for delays in creating a single airspace with member states, saying that many had fallen "significantly short of the overall level of ambition."
French Transport Minister Frederic Cuvillier said in a statement that he and his German counterpart Peter Ramsauer had written to Kallas setting out their "reservations" about the plans.
"France does not support the new European Commission plan," he said.
Around 1,800 flights were cancelled in France today due to the three-day strike.
Separately controllers in 11 countries will stage protests tomorrow, such as working to rule, the European Transport Workers' Federation said.
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