The charges were filed against Graham Spanier Thursday in connection with the Jerry Sandusky molestation scandal.
Spanier has been placed on leave and served as president of the university for 16 years.
State Attorney General Linda Kelly says additional charges have also been filed against Athletic Director Tim Curley and retired Vice President Gary Schultz, who were both charged last year with perjury and failure to properly report suspected child abuse.
Kelly says that an investigation showed that all three of the defendants had knowledge of the Sandusky shower assaults on young boys as the 1998 incident.
The case is set for trial in January.