The horse meat was found at a Silvercrest Foods facility in Ireland, CNNMoney reported.
Silvercrest supplied beef for Burger King restaurants in the United Kingdom, Ireland and Denmark.
"[W]e are deeply troubled by the findings of our investigation and apologize to our guests, who trust us to source only the highest quality 100 percent beef burgers," Burger King's vice president for global quality, Diego Beamonte, said in a statement.
Horse meat was discovered is Silvercrest in early January by Ireland's Food Safety Authority, which said the meat did not pose a safety risk.
Since that discovery, Silvercrest has made a "total management change" at the facility, said Paul Finnerty, CEO of Silvercrest parent ABP Food Group.
"We are proud of our excellent reputation for quality and service throughout Europe and are determined not to allow the Silvercrest incident overshadow what is a great business," Finnerty said.