Flights were canceled in and out of the northern German cities of Bremen and Hamburg, and the capital, Berlin, as workers went on strike on Monday.
Airport staff embarked on the walkouts called by the Verdi trade union in a dispute over pay for working nights, weekends, and bank holidays.
Berlin airport said in a notice that 200 flights would be canceled Monday, affecting around 27,000 passengers.
Hamburg airport said that all departing flights were canceled and nearly half of arrivals were too, while Bremen airport said there would no flights from the airport.
Germany's airport association, or the ADV, said around 45,000 passengers were directly affected as a result of the strikes.
The walkouts by airport staff come amid diffcult pay talks for employees of Germany's federal and municipal governments.
A winter of strikes
German unions are seeking a 10.5% pay raise, while employers have offered an increase of a total of 5% in two stages and a one-off €2,500 ($2,630) payment per employee.
Unions have rejected the offer, saying they were insufficient to meet expenses. The next round of talks is due to begin on March 27.
Additionally, there are negotiations nationwide over payments for air safety workers, and locally for ground service workers.
But Germany is not the only one to have been affected by strikes. In the UK, hundreds of thousands of people, including teachers, university lecturers, train and bus drives, staged a walkout last month to demand higher wages to meet rising living costs.
In France, more than a million demonstrators marched in cities and towns last week against the government's plan to raise the retirement age to 64.