The 27-year-old was taken off at half-time of the 2-2 Champions League draw with Club Brugge with what Madrid described as a stomach problem.
The club was forced to deny Courtois had become ill due to anxiety, having conceded twice to Brugge in the first half to compound a difficult run of form at club level.
Martinez says Courtois is still recovering from illness and insists he is the world's best in his position.
"It wasn't true that he had anxiety," Martinez said."He is still feeling the effects of a stomach bug and needs to regain a kilogram or two. That's what can happen with a stomach bug.
"He is a player who dreamed of playing for Real Madrid from a young age and he is ready to define an era there. I am convinced that he is the best goalkeeper in the world."