Cassandra Lynn Ursrey, 51, used her position as payroll coordinator for Clayton-Waycross to create false payroll entries over a seven-year period that she used to take the money, the indictment says.
The company, a division of CMH Manufacturing Inc., makes prefabricated modular buildings in Waycross.
The indictment that was issued Wednesday says false time entries were created for more than 750 former Clayton employees from 2003 to 2010.
The company issued more than 2,000 payroll checks based on those entries, which were collected, falsely endorsed and cashed, the indictment says.
If convicted, Ursrey could be sentenced to 20 years in prison on the mail and wire fraud charges and consecutive two-year prison terms on each of the charges of aggravated identity theft. She is also subject to $250,000 fines on each count.