By Friday morning 50 flights had been cancelled in Düsseldorf, a spokesman from the airport said. There are 560 planes scheduled to land or take off from the important hub during the day, but it is not yet clear how many will be affected.
At nearby Cologne/Bonn Airport, 26 flights had already been cancelled. Airlines have reportedly advised travelers to check ahead before heading to the airport on Friday. The airport normally would see 200 planes arrive and depart during the day.
Other German airports have been affected by the strikes, with Berlin Tegel reporting disruptions to flight service.
Trade union Verdi called all security staff to walk out on Thursday, leaving checkpoints essentially shut down, plunging both of the North Rhine-Westphalian airports into disarray and filling airports with long queues.
Across the two airports on Thursday around 200 flights were cancelled and many more were delayed.
Union representatives want to push through their demand for a €14.50 hourly wage for security personnel, who currently earn €11.80 per hour.
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A similar one-day strike last week caused chaos in Hamburg. The trade union Verdi hopes targeting the airports in North Rhine-Westphalia will increase pressure on employers.