The alleged crime came to light in an email written by a close Madigan ally back in 2012.
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The document was just released this week by Gov. JB Pritzker's Office, and the governor spoke publicly about the allegations for the first time Thursday.
RELATED: Lawmakers call for investigation after email from Madigan ally reveals possible rape cover-up
Pritzker said he has ordered the state's executive inspector general to investigate and find out what the facts are and who is responsible for any crime.
"Well first of all, the subject of this email is horrific," Pritzker said about the email by former lobbyist Michael McClain, a longtime Springfield power broker and close ally of Madigan.
In the 2012 email addressed to top aides of then-Governor Pat Quinn, McClain pleads for leniency for Forrest Ashby, a state employee facing a disciplinary hearing.
McClain wrote "He has kept his mouth shut on Jones' ghost workers, the rape in Champaign and other items."
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"What I want to know is what is the rape that's being alleged here, what exactly are the circumstances around that, is there a cover-up that was done around that and secondly, what is this ghost payrolling reference to? Was there wrongdoing associated with that and who's responsible?" Gov. Pritzker said.
State Rep. Jim Durkin, the House Republican Leader, sent a letter to Madigan Wednesday asking for a committee to be convened to investigate the allegations.
"Let's ask these individuals to first voluntarily come before the committee under oath. If they don't, I've asked the speaker to issue subpoenas to compel their appearance before this committee. I'm not going to wait and say we'll leave it off to somebody else to investigate," Durkin said.
But after Madigan spoke with the governor Thursday, he sent a letter back to Durkin, declining to approve a House investigation.
He said, "Recognizing the sensitivity of the matter for any potential survivors, any investigation should be handled by the appropriate investigative entities without interference by the General Assembly."
Durkin called that decision disappointing but not surprising.
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Meanwhile, Champaign County State's Attorney Julia Rietz is asking local law enforcement to review files from 2012 to see if there was a reported rape or investigation.
No formal investigation has been launched yet, but Rietz said she is very concerned about the situation.
Ashby was on contract serving as a consultant for correctional training revisions as of last September, according to John Keigher, chief legal counsel for the Illinois Law Enforcement Training and Standards Board. He also worked on the campaign of JB Pritzker while he was running for governor.
The board suspended Ashby's contract Wednesday due to the investigation ordered by the governor, Keigher said.
Ashby and McClain didn't respond to ABC7's requests for comment, as of late Wednesday.