Illinois-based Walgreen Co. claims in a lawsuit filed in San Francisco Superior Court on Monday that the ban is unfair because it applies to pharmacies but not to grocery stores and so-called "big box" stores that contain pharmacies.
The company says that distinction violates the equal protection guarantees of the federal and California constitutions.
The ban on tobacco sales by pharmacies was enacted by the Board of Supervisors and signed by Mayor Gavin Newsom in August and is due to go into effect on Oct. 1. It was the first such city law passed in the nation.
Matt Dorsey, a spokesman for City Attorney Dennis Herrera, said lawyers for the city and Walgreens were meeting with a Superior Court judge this morning to set a schedule for briefs and a hearing on the company's request for a preliminary injunction.
The company has asked for a hearing by Sept. 30, before the ordinance takes effect.
Dorsey said, "We think the complaint is without merit and we'll be arguing that in greater detail in court."
The lawsuit contends the ordinance is "anti-competitive and unconstitutional, only prohibiting tobacco product sales at some pharmacies, but not others, favoring some retail establishments that have pharmacies but not others."
Walgreens is the largest drugstore chain in the nation, with more than 6,000 stores nationwide, including 54 in San Francisco.