The indictment claims that Nagin handed lucrative city contracts to consultants and contractors in exchange for more than $230,000 in bribes and kickbacks, including free granite for his family business, personal services and free trips.
Nagin, 56, is also charged with money laundering conspiracy and filing false tax returns from 2005 to 2008.
He faces between five and 20 years behind bars if convicted, along with hundreds of thousands of dollars in fines.
Michael Anderson, special agent in charge of the FBI's New Orleans Field Office, said the indictment "should serve as a reminder to current and former public officials that, in the interest of full accountability, the FBI pursues corruption even after an official leaves office."
Nagin, who gained nationwide fame as the public face of the tragedy that swept through his historic city, was said to have accepted about $72,250 in bribes from Rodney Williams and his company, Three Fold Consultants, LLC.