Wegmans has been fined $750,000 and a liquor store in Buffalo has also been fined.
The State Liquor Authority said Amherst Street Wine and Spirits is among five stores that let Wegmans set prices illegally.
Wegmans is allowed to sell beer in New York State, but not wine or liquor.
The SLA accepted a no contest offer that settled eight charges.
The liquor stores were fined $75,000 each.