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The airport said in a statement that 17 flights departing Munich were cancelled on Thursday night, affecting nearly 3,000 passengers, and 15 flights due to land were diverted to other cities, including Stuttgart, Nuremberg, Vienna and Frankfurt.
Affected passengers in Munich were offered camp beds, blankets, drinks and snacks, the statement added.
It did not specify when flights will resume.
Several people spotted drones around the airport at about 1930 GMT Thursday, and again an hour later, leading to the closure of both runways for an hour, the police spokesperson said.
German authorities have launched a search to identify the origin of the drones.
Police helicopters were deployed but "no information is available on the type and number of drones," the spokesperson said.
The incident comes ahead of the final weekend of Germany's Oktoberfest, which draws hundreds of thousands of people every day to Munich.