Mortier, who recently had started undergoing treatment for cancer and whose tenure wasn't set to expire until 2016, will be succeeded at the helm of the company by Joan Matabosch, who was the artistic director of the Gran Teatre del Liceu in Barcelona.
The appointment of Matabosch is effective immediately and his tenure will last for at least six years, the company said.
Matabosch's appointment hints at the growing tension between the company and Mortier, who recently told a Spanish newspaper that there were no qualified Spaniards who could fill his shoes. He also said that he would cut short his term if a successor was named who did not meet his approval.
It remains unclear whether Mortier was fired or voluntarily stepped down.
Mortier, who hails from Belgium, is one of the more colorful personalities in the classical-music world, having developed a reputation for embracing new, edgy works. He has headed some of the most prestigious classical-music organizations in the world, including the Salzburg Festival and the Opéra National de Paris.
In 2008, Mortier was supposed to join the New York City Opera as its new general director. But he quit his post before he even started after the company cut its budget following the global financial crisis.
During his tenure in Madrid he championed new and edgy work. The company recently premiered Philip Glass' new opera "The Perfect American," which depicts the final days in the life of Walt Disney.
A new opera based on the short story "Brokeback Mountain" is scheduled to premiere in January.