Twenty-one scheduled departures from Catania had to be scrapped and 26 arrivals re-routed to alternative destinations. The smaller airport of Comiso in the area was also closed down.
Sac, the company that manages Catania airport, said in a statement that "the wind direction and intensity" meant the ash was a risk to flights and it had to close off its air space. Sac said it will review the situation on Monday.
Etna is an active volcano and eruptions are frequent but the latest activity, which began on Saturday, is the most intense in months.
The lava flow down one side of the mountain is visible from Catania and Taormina, a popular seaside resort. Three small earthquakes were also registered around the volcano on Sunday.
Watch a timelapse video of Enta erupting last month: