The Belgian goalkeeper's spell with Atletico is currently in its third season but Chelsea manager Jose Mourinho recently suggested that he would not be returning to Spain after the current loan deal expires.
"I do not know why he said that," Villaverde told reporters. "You would have to ask him.
"I can say that we are very happy with Thibaut and that Atletico Madrid will do everything possible for him to stay with us. Normally when I negotiate with Chelsea, or any team, it is not a negotiation with the coach. Never."
Courtois recently revealed that he is waiting to hear what Chelsea's plan is for his future.