Reports in Germany on Friday morning suggested Lewandowski had signed a pre-contract with the Bundesliga champions and would move south either this summer - should Bayern agree a fee with Dortmund - or in 2014 when he becomes a free agent.
But a Bayern statement read: "FC Bayern, contrary to these reports, do not have any contract with Robert Lewandowski."
Dortmund insist they have not received an offer for the Poland international and have put a new deal to the 24-year-old following his virtuoso display on Wednesday, in which he scored four times in a 4-1 victory against Real Madrid.
"It would be negligent of us not to try to keep probably the best striker in Europe," general manager Hans-Joachim Watzke told the Bild newspaper.
"It's true that we have discussed new conditions once again."