The 22-year-old was a substitute for La Roja in a European Championship qualifier in September 2014 but now wants to play for Morocco, his parents' country of origin.
FIFA rules bar players from switching allegiance once they have played a competitive international even if they hold dual nationality.
"The Court of Arbitration for Sport (CAS) has registered an appeal filed jointly by the football player Munir El Haddadi and the Moroccan Football Federation against the Fédération Internationale de Football Association (FIFA) and the Spanish Football Federation," a CAS statement said.
"Munir El Haddadi and the Moroccan Football Federation are challenging the decision issued on 13 March 2018 by the FIFA Players' Status Committee in which their request to have the sporting nationality of Munir El Haddadi changed from Spain to Morocco was rejected.
"A CAS arbitration procedure is in progress. The Appellants have requested that the Arbitral Award be issued by mid-May in order for the player's sporting nationality to be decided prior to the commencement of the FIFA 2018 World Cup."
Spain and Morocco have been drawn in the same group at the 2018 World Cup in Russia, alongside Portugal and Iran.