Lewandowski's contract expires in 2014 and there has been no indication from the player that he will be extending that deal.
The chances of him being sold in the summer, one year before he becomes a free agent, are high, but general manager Hans-Joachim Watzke denies a deal has already been struck with Bayern.
"It's just a bubble of speculation," he said. "There is absolutely zero substance in the reports, there's is not even a primary source - that really gets on my nerves.
"The fact is, Robert has a contract with us until 2014 and we want to extend that."
Reports in Germany and Italy on Tuesday claimed Lewandowski had already agreed terms with the Bavarians and the two clubs would now discuss a fee for the Poland international.
Watzke has rejected the claims, but admits his club would never stand in the way of a player who wants to leave.
"If Robert doesn't extend his contract by the end of the season, then we will just do what we've always done, which is sit down together and discuss where things go," he told the Spiegel magazine.
"But we certainly wouldn't let him go for any old price."
Lewandowski has score 18 goals in 28 matches for the Westphalians this season, attracting interest from other top European clubs with his performances in the Champions League as well as his consistent success in the Bundesliga.