SAN ANTONIO - H-E-B has paid $12 million to settle a whistleblower lawsuit accusing the San Antonio-based grocery chain of Medicaid fraud.

Since at least 2006, according to the suit, H-E-B allegedly submitted to Texas Medicaid inflated prices on thousands of claims for prescriptions it filled so the company could obtain higher reimbursements than allowed.

In the settlement agreement, H-E-B denied any wrongdoing. In a written statement, the company said it had an "arrangement" with the state regarding Medicaid pricing on certain drugs. It cited a combination of "systems changes and modification of the listed drugs" for "inadvertently" not passing on the correct pricing "for a period of time."

"The settlement relates to the interpretation of a specific regulatory requirement that applies only to the Texas Medicaid program," H-E-B said in its statement. "While the interpretation of this regulation is not free from doubt, we agreed to resolve this matter in the best interests of our state and H-E-B."

The settlement amount represents less than 1 percent of the business H-E-B did with Texas Medicaid during the time period, before legal fees, the company said. "There were no penalties assessed."

The whistleblower suit was brought in 2011 in Travis County by three pharmacists who worked in other states where they filled prescriptions for H-E-B customers. The pharmacists weren't H-E-B employees.