By Ellen Wulfhorst

(Reuters) - The former president of Pennsylvania State University filed suit on Wednesday against the author of a scathing report on the school's child sex abuse scandal, saying the investigation disregarded evidence and reached false and damaging conclusions.

Graham Spanier, who faces criminal charges stemming from the molestation case involving former Penn State assistant football coach Jerry Sandusky, alleges in his complaint that the report's author, former FBI Director Louis Freeh, intentionally defamed him and harmed his reputation.

The July 2012 report by Freeh accused Spanier and other Penn State officials of covering up Sandusky's sexual abuse of children for years in an effort to protect the university's multimillion-dollar football program.

Sandusky was convicted in June 2012 of sexually abusing 10 boys over a 15-year period. Now 71, he is serving a sentence of 30 to 60 years in prison.

Spanier, who was fired in November 2011, is awaiting trial on charges of perjury, obstruction of justice, failure to report suspected child abuse, conspiracy and endangering the welfare of children.

He has denied any role in a cover-up, saying he never learned of Sandusky's misconduct until 2011 when the former coach was indicted.

His complaint calls Freeh's investigation "glaringly deficient and grossly inadequate" and said investigators purposefully avoided interviewing witnesses who would have cleared Spanier.

They were "determined to transform Dr. Spanier from a preeminent academic administrator to a conspirator who enabled a serial pedophile," it said.

Freeh accused top school officials of a cover-up that began as early as 1998, when university police investigated allegations of abuse but let Sandusky off with a warning.

The report also accused famed Penn State head football coach Joe Paterno of helping cover up Sandusky's sexual abuse. Paterno died in January 2012.

"The Freeh report was little more than a public relations product that expediently scapegoated a few individuals and was designed to knock the controversy out of the news as quickly as possible," Libby Locke, an attorney for Spanier, said in a statement.

Freeh could not immediately be reached for comment.

The defamation complaint, filed against Freeh and his law firm, Freeh Sporkin & Sullivan, in the Court of Common Pleas in Center County, Pennsylvania, seeks unspecified compensatory and punitive damages.

The Freeh report was commissioned by the Penn State Board of Trustees at a cost of $6.5 million.

(Reporting by Ellen Wulhorst in New York; Editing by Peter Cooney)