Frankfurt am Main - Hundreds of flights were cancelled at the three airports and up to 110,000 passengers may be affected.
"Customers are being rebooked to their final destination and will receive the updated itinerary shortly. Customers can view their updated itinerary on the website," the airline said in a statement.
News agency DPA reported that the walkout, slated to last from 3:00 am (0200 GMT) to midnight (1100 GMT), was expected to affect around 100,000 travellers.
At Cologne-Bonn, where 131 of almost 200 flights were cancelled, union Verdi told DPA the security strike was also slowing freight handling.
Representing 23,000 airport security staff across Germany, Verdi is demanding a pay increase to 20 euros ($23.08) per hour from the present rate of 17 euros, or almost 18 percent.
Employers' association BDLS meanwhile is offering increases of between two and eight percent.
Passengers' first taste of the pay dispute came Monday, when Berlin's two airports Tegel and Schoenefeld suffered "warning strikes" with around 50 departures cancelled.
The next round of Verdi and BDLS negotiations will take place on January 23.