The Portuguese has come under pressure since his side dropped four points behind Barcelona in the Primera Division title race and there were reports he could be set to leave the Bernabeu.
But Valdano claimed his comments had been misrepresented.
He told Marca: "You have interpreted my words as a message to the coach and I have done very bad things when it has been something that was never my intention and never intended.
"Mourinho has to drive us to achieve the greatest possible gains to be better than last year and hope to continue in this vein.
"Do not look for anything unusual, we have the logical relationship between a CEO and the first team."
Valdano revealed that any return to the club for Dutch striker Ruud van Nistelrooy would be completed this week.
He added: "We're on it. This week is going to be definitely one way or another."
