Controllers began returning to work yesterday afternoon but Public Works Minister Jose Blanco said it would take 24 to 48 hours for air traffic to return to normal.
The army was called in to take over control towers and the government threatened to take legal action against individual strikers who are locked in a long-running dispute over pay and conditions with the state-run airports authority AENA.
Passengers camped out in airports across the country on Saturday as the unofficial strike action caused chaos and threatened to deepen Spain's economic problems.
Spain is carrying out tough reforms and spending cuts to rein in a deficit and ward off market fears it may need a bailout similar to that of Ireland.
AENA said Spanish airspace had reopened by mid-afternoon.