The overnight disruption is the latest in a series of similar incidents that have rattled European aviation, raising concerns about deniable hybrid attacks on Ukraine's European allies, possibly directed by Russia.
As airport operations resumed early on Friday morning, a Reuters witness saw passengers checking in for a flight to Varna in Bulgaria, and the departure board showed only a few flights had been cancelled.
A flight from Bangkok was the first of the day to land after 5am on Friday, according to the airport's website.
The airport said several drone sightings late on Thursday evening had forced air traffic control to suspend operations, leading to the cancellation of 17 flights and disrupting travel for nearly 3000 passengers, who were provided with camp beds, blankets and food.
Another 15 arriving flights were diverted around the region.
Public broadcaster BR said local and national police were investigating the incident.
The drones were sighted in the late evening above the airport, a police spokesperson told newspaper Bild, but because it was dark, the sizes and types of the drones could not be determined.
Police did not immediately respond to Reuters' requests for comment.
The drone incidents follow airspace intrusions last week that temporarily shut airports in Denmark and Norway, which led European Union leaders at a Copenhagen summit to back plans to bolster the bloc's defences with anti-drone measures.
"Europe must be able to defend itself," Danish Prime Minister Mette Frederiksen said after the meeting.
Her defence minister spoke on Friday morning of a Russian "hybrid war against NATO and the West".
Authorities have not publicly blamed anyone for the Munich drone incident, but some European officials have suggested Russia was behind other recent airspace violations.
"Russia tries to test us. But Russia also tries to sow division and anxiety in our societies," European Commission chief Ursula von der Leyen said on Wednesday.
Russian President Vladimir Putin joked on Thursday that he would not fly drones over Denmark any more, but Moscow has denied responsibility for the incidents.
The airport disruption in Munich added to a tense week for the city after its popular Oktoberfest was closed temporarily due to a bomb threat and the separate discovery of explosives in a residential building in the city's north.
Friday is German Reunification Day, a public holiday.
