The Poland international's agent Maik Barthel stated on Thursday that the striker wants to leave BVB this summer and added they have already agreed personal terms with another club, leading to speculation that Lewandowski was set to join Bayern.
Nevertheless, the Bavarians have stressed that there is no truth in the reports claiming Lewandowski to the newly-crowned Bundesliga champions is a done deal.
"Bayern Munich have taken notice of various reports about Robert Lewandowski and want to make it clear that Lewandowski does not have a contract with Bayern," a statement on the Bayern website reads.
The 24-year-old attacker has a contract with Dortmund until the summer of 2014, but has told the Champions League semi-finalists that he has no intention of extending his deal.
Lewandowski is therefore widely expected to leave BVB at the end of this season, with Bayern leading the race for his signature ahead of Manchester United, Manchester City and Juventus.
Dortmund was dealt a huge blow earlier this week when star player Mario Gotze announced that he will leave the club for Bayern this summer.