Speaking to Der Spiegel, zur Hausen said the newly-agreed plans of the Christian Social Union (CSU) to water down the smoking ban would be "catastrophic."
He said it was known that nearly a quarter of all heavy smokers would die of lung cancer, not to mention other forms of cancer.
The CSU and the Free Democrats (FDP) are set to hammer out a coalition agreement to rule Bavaria this weekend following last month's state election. Although many details are still to be decided, both parties are agreed on relaxing the smoking ban.
Zur Hausen won the Nobel Prize for his work identifying the fact that the human papilloma virus causes cervical cancer, a discovery which led to the development of a vaccine.
He told the magazine he had regularly smoked cigars until 1970 when he felt the connection between tobacco and cancer had been proven, after which he abruptly stopped.