On Sunday morning, Spanier in a statement announced his unconditional support of Senior Vice President Gary Schultz and Athletic Director Tim Curley, who have both been charged lying to a grand jury in the case.
"I have complete confidence in how they handled the allegations about a former university employee," Spanier said. Late that night, however, following a private meeting of the trustees, both men stepped down.
"The statement did strike me as overly confident and perhaps a bit premature," said Barmak Nassirian, an administrator with the American Association of Collegiate Registrars and Admission Officers. "I figured he must know what he's doing and there must be a reason why he is so unconditionally supportive. "
Some experts have a hard time believing Spanier - a family therapist by training and sensitive to issues such as sexual abuse - would have made such an error.
"He would have very detailed knowledge about these cases and how they need to be handled and why," said Terry Hartle, senior vice president of the American Council on Education.
"The thing that troubles me about this is the only people really talking is the (attorney general) who has a very strong incentive to tell the story in a way to make their case seem as absolutely strong as possible. The university isn't really talking about this. The legal process in the end will determine the outcome as it should be."
Attorney General Linda Kelly Monday said Penn State Coach Joe Paterno was not a target of the continuing investigation, but pointedly declined to say the same about Spanier.
At the center of the probe is Sandusky who has been charged with sexually abusing boys.
According to the grand jury presentment, Curley had informed Spanier of an incident in 2002 involving "inappropriate conduct" between Sandusky and a youth in a campus shower, as reported by a graduate assistant. The graduate assistant told the grand jury that he had witnessed Sandusky anally raping the boy, who appeared to be about 10.
Curley, however, testified that the graduate assistant described the incident to him as "horsing around." Spanier testified he was told the same by Curley.Spanier approved a decision to ban Sandusky from bringing children into the football locker room. Law enforcement officials were never notified of the incident.
Spanier, according to the grand jury report, said he didn't know the identity of the staffer who reported the incident, but he was aware Schultz and Curley did not plan to notify law enforcement or other authorities.
"I am very baffled as to how this did not fall in the lap of campus police," said Allison Kiss, executive director of Security on Campus Inc., a national campus security group based in Wayne. "That's most concerning, given the age of the victim."
But whether it might cost Spanier his job is unclear.
"There are a lot of things within the system that need to be looked at," Kiss said. "Inevitably, in the role of a president of an institution, especially a large institution, you cannot have your hand in everything. But it's very important especially when we're talking about issues of student safety to be well aware of how reports are handled and know the chain that they go through."
U.S. Rep. Patrick Meehan, (R., Pa.) a former U.S. attorney who has been outspoken on campus safety issues, said he plans to ask the U.S. Department of Education to investigate whether Penn State violated federal law by failing to report and investigate the complaint.
Penn State's failure to act "may well have created the circumstance to allow later violations to occur," he said.
Some higher education experts, however, said any possible missteps in this incident must be weighed against Spanier's positive impact on the 96,000-student university that runs on an annual budget of $4.3 billion.
"This is an extremely successful long-term president," said Ronald G. Ehrenberg, director of the Higher Education Research Institute at Cornell University. "The question is if you have a wonderful leader who has done all of these things for the university and over this long period of time has had the support of the faculty and administrators, is this someone you want to give up on?"
Appointed president of Penn State in 1995, Spanier is among the highest-paid public college university presidents in the nation. His total cost of employment was $800,592 in fiscal 2010, according to the Chronicle of Higher Education.
During his tenure, the college has grown in enrollment and programming, including a 14,000-student jump in the last decade, and enjoyed a stable administration.
The university started a College of Information Sciences and Technology early on in Spanier's in tenure. In 2000, it completed a merger with Dickinson School of Law in Carlisle, and in January 2009 opened a $60 million law school building on Penn State's main campus. The building complements the law school site in Carlisle, which also got a $50 million renovation and expansion.
The university in 2009 opened a graduate School of International Affairs to further a goal of Spanier's to make Penn State more global.
Spanier and his wife have donated more than a million to the university.
Some alumni worry about the impact of the allegations on Penn State fund-raising, which has brought in $3 billion in philanthropic contributions during Spanier's tenure.
"I don't think it's going to help us going forward," said Dan Kohlhepp, an alumnus who formerly headed a fund-raising campaign for Penn State's Dubois campus. "I've talked to other alums. Our hearts are broken that this could happen ... I'm in a state of denial."
Of Spanier, he said: "Graham Spanier is everybody's best friend."
Contact staff writer Susan Snyder at 215-854-4693 or email@example.com