Australian media group B&T media quoted Boutros Boutros, the divisional senior vice president of corporate communications for the airline, saying it felt "overlooked" during the voting scandal that rocked football's governing body earlier this year.
"We are seriously thinking about not renewing our partnership with FIFA beyond 2014," Boutros was quoted as saying during the Emirates-sponsored Melbourne Cup horse race.
In May, Boutros told Reuters the airline was disappointed by the cash-for-votes scandal that has led to several officials being suspended from the game.
Former Asian football chief Mohamed Bin Hammam was banned for life after being accused of bribery during his failed attempt to become FIFA president. He has always denied the allegations.
Emirates has commissioned research into its association with FIFA to see if there has been any long-term damage to its brand, according to the report.
"Emirates has not yet commenced discussions with FIFA on the extension of our partnership agreement beyond 2014. Discussions will begin in due course," the airline said in a statement on Wednesday, without giving any more details.
The Gulf carrier sealed one of its biggest ever sponsorship deals worth $195 million with FIFA in 2006 to become its official sponsor until 2014.
FIFA President Sepp Blatter said in June the organisation has been in contact with two of its main sponsors over the corruption allegations but there had been no threats to pull out.
