Christopher B. Epps, a former state corrections commissioner in Mississippi, was arraigned in federal court on Thursday on charges of participating in a corruption scheme in which he received nearly a million dollars from a contractor who paid off Mr. Epps’s home mortgage and helped him buy a beach condominium.

A 49-count federal indictment unsealed Thursday documents a complex conspiracy dating to 2007 in which Mr. Epps is accused of receiving dozens of bribes totaling as much as $900,000 in exchange for directing lucrative state prison contracts to firms connected to Cecil McCrory, a local businessman and former state legislator. Both men pleaded not guilty Thursday before a federal magistrate in Jackson, Miss.

The bribes alleged in the indictment came at a time when one state prison, the East Mississippi Correctional Facility, which was operated by a private company with ties to Mr. McCrory, had degenerated into hellish chaos, according to advocates for inmates. Civil rights lawyers and medical and mental health experts who toured the facility this year say gang violence is frequent, medical treatment substandard or absent, and corruption common among corrections officers.

The indictment says that Mr. McCrory operated several companies that had contracts with the state, including for prison administration, commissary services and evaluating Medicaid eligibility across the state prison system.