A protest by Alitalia cabin crews coincided with an Italian air traffic controllers' strike meaning nearly 400 flights by the national carrier were cancelled.
The industrial action threatened to affect up to 7,000 soccer fans planning to fly to Wednesday's showpiece against Liverpool.
Civil air traffic authorities warned of a risk to public security.
''Not allowing these people to fly is a serious problem,'' said Vito Riggio, head of Italy's civil aviation authority.
Milan, along with Liverpool, have only been allocated 17,000 tickets for the match.
AC Milan's players flew to Athens yesterday.
REUTERS BJR BD1525