Lisa Shoemaker, a spokesman for State Auditor Stacey Pickering, reported the indictment.
Details are forthcoming.
Thweatt, 50, faces a July 25 arraignment, which is a hearing when he will enter a plea before a circuit judge.
Shoemaker said Thweatt got a call today about the indictment.
He was arrested April 17 stemming from an auditor's investigation that he allegedly had a district-owned air conditioning unit installed at a mobile home he owns in Starkville and changed a title to hiss name on a district-owned truck.
Thweatt is on paid leave from the school district. He remains free on bond.