She also announced additional counts against Curley and Schultz, who are awaiting trial in January on earlier charges that they lied about their knowledge of allegations against the former assistant football coach.
"This case is about three powerful and influential men who held positions at the very top of one of the most prestigious institutes in the nation," Kelly said. "Three men who used their positions at Penn State to conceal and cover up the activities of a known child predator."
In laying out their case Thursday, prosecutors pointed to several contradictions in Spanier's 2011 grand jury testimony, in which he testified he had no knowledge of the earliest investigations into Sandusky and had never had discussions on whether to report the former assistant coach to police.
Had he or his colleagues acted sooner, Kelly said, half of the 10 boys Sandusky was eventually convicted of molesting might have been spared.
Curley, 58, and Schultz, 63, are expected to turn themselves in for rearraignment in a Dauphin County, Pa., court Friday. Spanier, 64, is expected to follow suit Wednesday.
Spanier's lawyers called Thursday's charges "a politically motivated frame-up."
Gov. Tom Corbett "has made no secret of his personal hostility toward Dr. Spanier," the lawyers said in a statement. "These charges are the work of a vindictive and politically motivated governor."
Corbett spokesman Kevin Harley said, "Spanier's statement is the ranting of a man who has just been indicted for covering up for a convicted pedophile."
Lawyers for Curley and Schultz said they had not fully reviewed the new charges and declined to comment. They filed a motion Thursday asking a judge to dismiss the earlier cases against them.
For Spanier, Thursday's criminal charges represent the nadir of a tumultuous year that began with Sandusky's arrest on charges he molested multiple boys, often on Penn State's campus. Sandusky was convicted in June and sentenced last month to a minimum of 30 years in prison.
After 16 years at the university's helm, Spanier was ousted by the Penn State board last November for his handling of the scandal. This summer, he became the chief villain in an investigative report by former FBI Director Louis Freeh that accused him and others of covering up Sandusky's crimes.
Freeh's report and the current charges lean heavily on a series of email exchanges among Spanier, Curley and Schultz that suggest the three were far more aware of past allegations against Sandusky than they have admitted.
Prosecutors alleged Thursday that those missives also showed the three were more concerned with covering up any untoward behavior by the former coach than reporting it to authorities.
The email traffic among the men centered on two early reports from Sandusky accusers.
The first was in 1998, when the mother of an 11-year-old accused Sandusky of inappropriately touching her son in a campus shower.
The second followed three years later when then-graduate assistant Mike McQueary allegedly told Curley, Schultz and then-head football coach Joe Paterno that he saw Sandusky molesting another boy.
In both cases, prosecutors said, the allegations set off a flurry of internal activity but resulted in no action that might have stopped future abuse.
"They had concerns for the university, they had concerns for each other, and they even had concern for Jerry Sandusky," State Police Commissioner Frank Noonan said. "But the one fact that you'll find lacking is any concern for the children who were victimized."
According to the presentment, Curley, Schultz and Spanier kept close tabs by email on the 1998 investigation conducted by Penn State and State College police.
No charges were ever filed in the case. A 95-page investigative report on the incident was filed separately from other criminal investigations. Then-Penn State Police Chief Tom Harmon told grand jurors that it was kept hidden for fear "the media might make inquiries," the presentment states.
Spanier testified before a grand jury in April 2011 that he had no knowledge of the 1998 incident.
When McQueary's allegations surfaced in 2001, Curley, Schultz and Spanier planned a response even before talking to the graduate assistant, grand jurors said.
The three men told a grand jury last year that they believed that McQueary's allegations described activity that was "horseplay."
Emails referenced in Thursday's presentment suggest they understood at the time that they were dealing with something more sinister.
In one, Spanier worried that the university might become "vulnerable" should Sandusky not be reported to police. It was agreed, however, not to do so.
The former university president told grand jurors in 2011 that he had never discussed whether the incident should be reported to child protection authorities.
Thursday's presentment also takes issue with the administrators' actions after the attorney general's office launched its investigation of Sandusky in 2009.
Early on, prosecutors issued subpoenas to Penn State for information concerning Sandusky and "inappropriate contact with underage males." It took nearly two years for the university to fully comply.
It was only after Curley and Schultz were arrested and Spanier had been replaced that investigators were able to uncover the email traffic among the men, prosecutors said.
Authorities also learned of a "secret file" that Schultz kept on Sandusky.
The charges against Spanier raised anew the question of whether Paterno, too, might have been criminally liable in the case.
Asked Thursday whether Paterno might also be facing charges had he not died of lung cancer in January, Kelly declined to speculate.
Noonan, however, reiterated his opinion that although Paterno had met his legal obligations in reporting the Sandusky allegations to his superiors, his decision not to follow up constituted a moral failure.
"What he did, what he didn't do, Joe Paterno, you guys can decide," he said. "The point is, we have the president, the athletic director, I mean the actual top people, and that's who we have charged."