The aircraft, with 380 passengers on board, was just 20 minutes into its flight from Sydney to Dubai and climbing at an altitude of 10,000 feet when it experienced a problem with one of its four engines.
"Emirates flight EK413 from Sydney to Dubai on 11 November turned back shortly after take-off due to an engine fault. Passengers are being re-booked on alternative flights," the airline said in a statement on Monday.
A mid-air engine blow-out in November 2010 on an A380 using Rolls Royce Plc Trent engines prompted Australia's Qantas Airways Ltd to ground its entire fleet of Airbus superjumbos for nearly a month.
Emirates, with the world's biggest A380 fleet, uses rival GP7200 engines built by Engine Alliance, a joint venture between General Electric Co and Pratt & Whitney, a unit of United Technologies Corp.
Engine Alliance said it was trying to determine the cause of the failure.
"The Engine Alliance is investigating root cause of the engine event and will initiate prompt corrective action," the companies said in a statement.
An Airbus spokesman said the company is working with the engine makers and Emirates to determine the cause.
Passengers on the giant double-deck aircraft, manufactured by Airbus parent EADS, said the superjumbo experienced a "judder" and then they saw flames shooting several metres out of one of the engines.
"I saw a flash. I thought it could have been lightning, but then we saw flames come out of the engine. The whole interior of the A380 lit up," passenger John Fothergill, 49, from New Zealand told Australia's Daily Telegraph newspaper.
Emirates later said there was no fire, although "passengers may have seen a flash."
The Dubai-based carrier apologised for the inconvenience to its passengers and said their safety was "of the highest priority and will not be compromised."
Superjumbos, worth $375 million apiece, typically carry around 525 passengers.
The A380, manufactured in Toulouse from parts sourced across Europe, have also been affected by cracks in the wings of a small number of aircraft.
There are eighteen airlines currently using the aircraft with total orders outstanding for 262.
(Reporting by Rob Taylor; Editing by Ryan Woo and Andre Grenon)
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