The Poland international is constantly being linked with a £24million summer move to Manchester United but Watzke suggests the exit would only occur for money and not because the player wants out.
"As often as I am talking to Robert, I do not have the impression he wants to leave us," Watzke told Sport Bild.
"We will have to make decisions in this case at the end of the season. We may decide on economical factors.
"Would it be best to cash in a big fee? Or would it be even better to keep Lewandowski to ensure we are more likely to qualify for the Champions League with him in our side, as this would guarantee us big income?
"It's a decision we will have to take. It's our decision. It's not something to be decided by others."