Investigators say the operation ran for weeks out of the Old Corner Saloon in Clements, which has a population of 941.
The local sheriff's office got a tip that fake vaccine cards were being manufactured and sold out of the bar, complete with laminations.
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Investigators with the California Department of Alcoholic Beverage Control then took over.
"Undercover agents with our Special Operations Unit were able to purchase multiple cards in April," said Luke Blehm, deputy division chief at the Alcoholic Beverage Control.
"As a result, we also observed several sales of fraudulent COVID-19 vaccination cards to other patrons," Blehm said.
Investigators say the cards were being sold for $20.
The bar owner, 59-year-old Todd Anderson, was charged with falsifying a medical record, falsifying a seal, several counts of identity theft and possession of a loaded, unregistered firearm, authorities said.
ABC News contributed to this report.