The Spanish giants have released a statement explaining the situation, following suggestions they owe money to the doctor embroiled in the 'Operation Puerto' investigation
Fuentes' lawyer made the claims during the 'Operation Puerto' investigation, which alleges that the doctor was involved in one of the most extensive drugs rings in sporting history.
But Los Blancos have told Europa Press news agency that the debt is related to "travel expenses and his wages" when he was called to give evidence in the trial against the French newspaper Le Monde in 2009.
In 2006, Le Monde accused Real Madrid, Barcelona and other football clubs of being linked to a plot involving Fuentes and doping.
The newspaper was ordered to pay €300,000 and €30,000 to Alfonso del Corral, Madrid's director of medical services, for 'meddling in honour' over their unsubstantiated claims.
Madrid released a statement on their website on Friday night to clarify that their only contact with Fuentes came when he was called as a witness in the aforementioned trial.
The Spanish club also revealed their intention to take legal action against the doctor after Fuentes let it be known to reporters that he was owed money by Madrid, but refused to elaborate on the reasons behind the debt.
"Given the attempt at confusing public opinion over his relationship with the club on the part of Eufemiano Fuentes, with evident bad faith and the aim of damaging the image of the club, Real Madrid CF will present a lawsuit with immediate effect," the statement concludes.