The findings are based data gathered by the department's undercover investigators.
Consumer Services Commissioner Caroline Orzac Shoenberger says Walgreens had the most store locations cited. Of its 123 area stores, 84 were cited for overcharging.
Thirty-seven Oscos and eleven CVS outlets charged more than the posted price at the checkout.
City investigators say they didn't find evidence the overcharges were deliberate.
Experts say consumers often don't notice they've been overcharged because prices are posted in aisles, and not on products.