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The owner of two pharmacies in Alabama has pleaded guilty to charges of obstructing a Medicare audit. He will pay a $2.5 million government penalty.

Rodney Dalton Logan, 63, was charged with trying to stop a 2012 federal audit of Medicare claims submitted by his pharmacy, Leighton Pharmacy Inc.

CVS/Caremark Inc. was an auditor on Medicare’s behalf related to prescription drug claims for Medicare Part D. Part D prohibits reimbursement to pharmacies for compounded medications made using bulk pharmaceutical powders.

Both of Logan’s pharmacies had retail and compounding components. The pharmacies sold Part D reimbursement for compounded medications, such as bulk powers, which is prohibited under Part D, authorities said. Logan responded to the 2012 audit by submitting falsified or misleading documents, which led to an investigation by FBI, HHS-OIG and FDA-OCI, according to court documents.

The deal was announced last month, but Logan officially pleaded guilty Thursday.