When air travel plunged following the global recession in 2008, Spanish air-traffic controllers suffered little impact: They were earning, on average, a half a million dollars apiece.

Last year, as the Spanish government tried cutting those payouts to below $300,000—still 10 times Spain's average salary—controllers protested by staging wildcat strikes during December holidays.

Socialist Prime Minister José Luis Zapatero, normally a friend of organized labor, called in the army to force controllers back to work before Christmas.

Spain's fight with its air traffic controllers is just one of many hurdles Europe faces in removing national boundaries in its skies. On the ground, the European Union erased most borders to movement of people and goods more than a decade ago. In the air, 50 years of rhetoric and 10 years of planning have yielded little progress.

Now, the EU is making another big push for what it calls the Single European Sky. Starting next January, Brussels aims to create the equivalent of aviation expressways and sweep away needless air-traffic bureaucracy. But this means shattering cozy fiefdoms, forcing national aviation agencies to cooperate and compelling controllers to work more efficiently—all without compromising safety. Controllers and managers at the national agencies are putting up a fight.