It is not known how many flights leaving from or arriving in Spain have been delayed, but around half of the 29,500 scheduled for today are expected to be late, according to the European Organisation for Air Travel Safety, Eurocontrol.
All flight plans presented before 10.26 GMT (12.26 midday mainland Spain time) were refused due to a breakdown in the ETFMS flow-control system which is used to regulate flights across Europe.
The problem, which has since been identified and is being fixed, means airspace has to be limited by up to 10% as a precaution.
Eurocontrol says air traffic is expected to return to normal by late tonight.
The agency assures that the mechanical breakdown does not pose any risk to passengers.