The aerospace giant will "change its pace of its deliveries by delaying the delivery to Emirates of six A380 planes from 2017 to 2018 and six others from 2018 to 2019," it said in a statement.
Despite the delay, Airbus restated its aim announced earlier this year of delivering 12 planes annually from 2018.
In November, Emirates complained of "technical difficulties" with the Trent 900 engines produced by British firm Rolls Royce for the A380.
In April 2015, Airbus selected Rolls Royce for the lucrative deal to provide the engines for 50 of its A380s that was worth a record at the time of $9.2 billion.
Emirates, the biggest client for superjumbos, took delivery of its A380 in November and has ordered 142 in total.
A380s with the Rolls Royce motor are already being operated by other airlines such as Qantas and Singapore Airlines.