(CNN) -- Prosecutors say Gary Schultz, a former Penn State vice president who oversaw campus police, held a file that detailed alleged incidents pertinent to the investigation of former football coach Jerry Sandusky, who faces more than 50 counts involving sexual acts with 10 boys since 1994.
Schultz and Tim Curley, Penn State's former athletic director, have pleaded not guilty to charges of perjury and failing to report an alleged sexual assault of a child.
The file, which prosecutors say was initially withheld during the investigation, shows inconsistencies with what Schultz and Curley told a grand jury, according to court documents filed by prosecutors and obtained by CNN on Tuesday.
Prosecutors say e-mails from Schultz, Curley and others further contradict that testimony.
"The commonwealth is entirely justified in using those documents as evidence to support the charge of Perjury against Schultz," the court documents say.
Tom Farrell, Schultz's attorney, said, "To be clear, Mr. Schultz did not possess any secret files. All his files were left behind after he retired and were available to his secretaries and his successor. The only 'secret' information revealed was the privileged grand jury information inaccurately described by unidentified law enforcement sources to the media."
Curley, 57, is on leave, and Schultz, 62, retired after the allegations. Days after the grand jury presentment against Sandusky came to light, Penn State ousted President Graham Spanier and head football coach Joe Paterno amid criticism they could and should have done more.
Curley was not immediately available for comment.
Penn State said in a statement Tuesday that it "has responded to several subpoenas and gathered documents from many sources across the institution."
"As soon as any relevant documents were discovered, the university immediately provided them to the office of the attorney general and the Freeh Group," it said. "Out of respect for the ongoing legal process, the university cannot discuss specific information as it pertains to these issues."
The firm representing Louis Freeh, a former FBI director investigating the university's handling of the scandal, also said Tuesday that his office "discovered these e-mails in the course of its work."
"These e-mails were then provided to the State Attorney General, consistent with the investigation's prior commitment to share certain information," the firm said. "These materials will be fully discussed in the report to the task force, and beyond that Judge Freeh and the investigation team has no further comment."
CNN's Susan Candiotti contributed to this report.