Graham Spanier sued May 25 to obtain old emails that he says are necessary to respond to Penn State's child sex-abuse probe.
According to the Centre Daily Times, the university contends it can't disclose the messages because of an ongoing investigation by the state attorney general.
Documents filed by Penn State on Thursday in Centre County court also argue that Spanier should have first requested the emails under the state's Right-to-Know law.
Penn State is conducting an internal investigation of how the university handled child molestation allegations against former assistant football coach Jerry Sandusky.
Sandusky is currently on trial and has denied wrongdoing.