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 Spanish 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 euros to Alfonso del Corral, Madrid's director of medical services, for 'meddling in honor' over their unsubstantiated claims.
Follow GOAL.COM on Twitter