At Germany’s third biggest airport in Duesseldorf, some 94 flights were cancelled during the morning, out of a total of 528 arrivals and departures scheduled for the day, according to information from the airport.
The affected flights were predominantly serving domestic routes but did include some European destinations.
And at Cologne-Bonn airport, also in the west of the country, 12 departures out of 80 had been cancelled.
The giant services union Verdi called the strike, which began at 4:00 am (0300 GMT) and was to go on until midnight, and has already warned that stoppages will resume on Friday.
Similar action by security personnel in December also led to flight delays and cancellations at several German airports.