The airline, which paid out $195 million to become a Fifa 'partner' from 2007 to 2014, says it is "disappointed" by the corruption allegations that have plagued Fifa in recent weeks.
"Emirates, like all football fans around the world, is disappointed with the issues that are currently surrounding the administration of this sport," said Boutros Boutros, senior vice president of corporate communications at Emirates.
Mohamed bin Hammam of Qatar, president of the Asian Football Confederation, was suspended by FIFA's ethics committee on Sunday, along with three other officials. They are accused of offering bribes to other officials to secure the Fifa presidency for Mr bin Hammam. Sepp Blatter, the president of Fifa, was cleared of any wrongdoing.
The Dubai airline is the latest of several sponsors to voice concern about the corruption probe at Fifa.
Coca-Cola, which also has 'partner' status with the football association, said that the bribery allegations are "distressing and bad for the sport", the Financial Times reported. Another headline sponsor, Adidas, said that the surrounding publicity was "neither good for football nor for Fifa and its partners".
Mr Boutros said that he hoped the issue would be resolved.
"Emirates' sponsorship of all Fifa Tournaments, including the Fifa World Cup, aims to help promote football and ensure that it is accessible to the billions of football fans; something Fifa has managed to do extremely well in recent years," he said.
"We hope that these issues will be resolved as soon as possible and the outcome will be in the interest of the game and sport in general."