The strike, which began on Wednesday and is expected to end on Thursday, was called against a European Commission proposal to reduce air navigation costs.
The unions have labelled the reductions, which are part of a programme called Single Sky Europe, excessive.
EU air navigation body Eurocontrol has announced that Portugal and Italy are so far the two countries most seriously affected by the air traffic controllers strike, Spanish news agency Europa Press reported.
Other nations hit by the strike include Greece, France, Slovakia, Czech Republic, Hungary and Austria.
Spain’s air travel association AENA has released a statement claiming that air travel within Spain won’t be hindered, although three Ryanair flights to the Italian cities of Venice, Milan and Bologna have already been cancelled.
Passengers should check with their airlines to find out if their flight has been cancelled or changed.