The Algerian duo demanded the presence of Omar Dabo and Moussa Coulibaly respectively to play in the local cup semi-finals on Friday.
"It’s outrageous. FIFA say no discrimination in soccer but when it comes to Real Madrid and Sevilla they say yes and now when it’s Mouloudia and JS Kabylie they say no," said Mali boss Jean-François Jodar to football365.fr.
"Apparently it’s good being strong and rich than poor and weak in the World of football and that’s something very dangerous," added the French tactician.
The case blew up in the past few days as 21 African players had to leave their Spanish teams, who are still in action, to join their national teams’ campaigns in the African qualifiers.
Real Madrid, Sevilla and Barcelona wanted to keep Diarra, Kanoute and Cameroon's Samuel Eto’o respectively as this round is crucial in determining the league winner.
Mali also are in big need for their stars to boost their chances and book a place in next year's Ghana finals.
FIFA gave their controversial verdict on Thursday, saying that Diarra and Kanoute can play for clubs this weekend as the Spanish league fixtures have been set before the African governing body CAF announced their schedule.