At Hamburg airport, all flights were halted at 06:10 am (0410 GMT) after several Letzte Generation (Last Generation) protesters breached the security fence and glued themselves to the runway.
The airport said it had been forced to scrap 17 arrivals and 19 departures before resuming operations, but warned of further delays throughout the day.
"We can confirm that a group of people gained unauthorised access to the airport premises," the airport said in a statement.
"For security reasons, air traffic had to be temporarily suspended. At 9:50 am, flight operations were resumed," it said, adding that police had been called to the scene.
The protest coincided with the start of summer holidays in Hamburg, with more than 330 flights scheduled carrying over 50,000 passengers.
Duesseldorf airport, Germany's fourth largest, likewise warned of delays and flight changes after several activists glued themselves to the runway.
The Letzte Generation group said in a statement it was protesting against the government's "lack of a strategy" to combat the climate crisis.
"The government has no plan how to reduce emissions sufficiently, thus openly breaking climate protection legislation and letting us all walk into climate catastrophe," Micha Frey, one of the protesters at Duesseldorf airport, was quoted as saying in the statement.
The Letzte Generation activists, known for gluing themselves to roads to draw attention to the climate emergency, have divided public opinion with their tactics.
German prosecutors raided the homes of several activists in May as part of a probe over suspicions they were "forming or supporting a criminal organisation".
Activists have also been fined for disrupting traffic or obstructing police, and some have received jail time.
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