The Poland striker has long been touted with a move to the Allianz Arena and the coach claimed after Saturday's Champions League final win that the 25-year-old will be "hanging about too much".
Watzke says that the former Real Madrid trainer should stay out of the saga and claimed that the Bavarians have not approached the club over a move for the player.
"Jupp Heynckes should stay out of this and concentrate on the lineup for next Saturday [for the DFB-Pokal final against Stuttgart]," he told reporters.
"I don't know how close Heynckes is to the management of Bayern. But if they want to have Lewandowski it would be good if we were told about this."
For his part, Lewandowski is remaining tight lipped on his future, adding: "Now I will have a break for four or five days, then I will go to the national squad."
Bayern faces Stuttgart on June 1, hoping to complete the club's first treble.