The disruptions affect both cargo and passenger flights and come just one day before world leaders gather for the annual security conference in Munich.
According to a trade association for German airports, 460 flights have been canceled, which are estimated to directly affect around 69,000 passengers.
Lufthansa, Europe's largest airline, is offering affected travelers rebookings.
The strike follows stalled negotiations between Lufthansa and the German unions Vereinigung Cockpit and UFO.
