Airports in Zurich and Geneva began to ramp up service on Wednesday after a technical problem with the air traffic control system halted takeoffs and landings for hours.
"Flight operations at Zurich Airport are running again. Flight operations are planned at 50% capacity until 09:30 (0730 GMT), and at 75% capacity from 09:30," it said in a statement.
It advised passengers to refer to airlines' flight information.
Pan-European air traffic agency Eurocontrol warned airlines in a bulletin to expect "high delays".
Geneva Airport said air traffic had gradually resumed since 8.30 a.m.
Several flights had been cancelled, it said on Twitter, telling travellers to check with their airlines to see if their flight is still on.
Earlier, air traffic control agency Skyguide said it had closed Swiss airspace to ensure safety after a technical malfunction.
Zurich airport had scheduled 330 flights and Geneva 211 on Wednesday, according to FlightRadar24 data.