The delays were necessary to protect passengers, officials said, but they hit thousands of travellers and cost airlines millions of dollars.
Drones pose a "threat to the flying public" and "to an aircraft in operation," said Ismaeil al-Blooshi, deputy head of the air safety department of the United Arab Emirates' civil aviation authority.
He compared drones to the threat posed by birds, but said they were less predictable and harder to avoid.
The cost of closing airspace for one hour runs into millions and creates a long backlog, but there is no room to compromise on safety, Blooshi said.
More From This Section
"The economic impact is not even on the table" when considering the risks, he said. "The number one priority is avoiding harm to passengers."
Drones have become a more common sight in the skies above the emirate as related technology has plunged in price, with professional photographers eager to use them.
After last year's incidents, operator Dubai Airports stressed that flying drones within five kilometres (three miles) of airports was illegal.
New regulations introduced last year stipulate up to three years in jail or a fine of 100,000 dirhams (USD 27,000, 25,000 euros) for flying a drone over a prohibited zone.