German newspaper Bild reported earlier in the week that the Poland international had already signed two contracts with Bayern, one that was due to start next season and one in 2014.
But a Bayern statement read: "FC Bayern, contrary to these reports, do not have any contract with Robert Lewandowski."
Dortmund insist they have received no offers for the 24-year-old, whose fine season continued on Wednesday when he scored all four goals in their 4-1 Champions League win over Real Madrid.
Their intention is to sign the prolific Pole to a new contract, with his current deal due to run out at the end of the 2013-14 season.
Dortmund's general manager Hans-Joachim Watzke said in Bild: "It would be negligent of us not to try to keep probably the best striker in Europe. It's true that we have discussed new conditions once again."
Lewandowski, who has scored 34 goals this season with 10 of those in the Champions League, has also been linked with a move to the Premier League with Manchester United chief among his suitors.
Dortmund have already suffered one high-profile departure with midfielder Mario Gotze announcing earlier this week he was using a release clause in his contract to join Bayern over the summer.
Talk of Lewandowski joining Gotze in leaving the Westfalenstadion intensified on Thursday when his agent claimed a deal had been agreed with an unnamed club.
"We have reached an agreement with a club and intend (him) to move this summer," Maik Barthel told Sport Bild, who suggested the club in question was Bayern.
"There is a very interesting offer for Robert which fulfils entirely the demands set by Dortmund and also the demands of Robert.
"Dortmund have assured us that Robert can move at the end of the season under these conditions.
"We stick to agreements and now it's up to the clubs to sort things out."