"We file what we file. We don't have any comment," U.S. Attorney Patrick Fitzgerald said.
Prosecutors allege in a 76-page court document Ryan knew his aides were shredding campaign documents in 1998 that showed misuse of state resources from copy paper to vehicles and cell phones for political purposes when Ryan was Illinois secretary of state from 1991 to 1999.
The ongoing "Operation Safe Roads" investigation has resulted in scores of convictions of current and former state workers who allegedly sold drivers' licenses for cash, some of which was diverted to Ryan's campaign fund.
Other politically connected state workers allegedly worked as Ryan's private campaign army at taxpayer expense but Ryan has repeatedly denied any wrongdoing.
Scott Fawell, the highest ranking former Ryan aide indicted on racketeering and fraud charges, told investigators Ryan knew two months before the election that campaign documents were being destroyed late at night. Ryan has not been indicted but Wednesday's court filing was the first linking him by name to potential criminal corruption.
Ryan declined comment on specifics of the investigation.
"As everyone knows, there are two sides to every story, two sides to allegations leveled by individuals to claiming to recollect conversations and actions from several years ago," Ryan said in a statement.
"I will only repeat what I have said many times before: My conscience is clear and, in every public office I have held, I have respected the public trust."
The shredding allegedly began in September 1998 when Fawell, fearing a federal raid on state offices, allegedly told secretary of state employee William Mack, Ryan's scheduler, to collect campaign material from work areas and destroy it. Mack testified he heard Fawell tell Ryan, "Hey George, I told Bill to go around and tell people to get stuff out of their offices."
Ryan reportedly said nothing and left the room.
The court filing said in October 1999, Fawell's former mistress and her then-husband burned several boxes containing campaign contribution and employee hiring records in a barbecue grill at their suburban home.
When swirling ash and smoke threatened to draw attention to them, they decided to store the material in the basement and put some boxes out for garbage pickup each week over the next two months.
New charges also were filed against Ryan political adviser Lawrence Warner for allegedly extorting $3 million in kickbacks from seven companies doing business with the state.
Ryan and his wife allegedly took five consecutive November vacations at the posh Jamaican estate of a suburban businessman who won a sweetheart lease for the secretary of state's license facility in South Holland. Ryan said he paid for the Caribbean trips.
Ryan's former inspector general and childhood friend Dean Bauer pleaded guilty to corruption charges for blocking investigations of suspected stealing of state funds to buy campaign fundraising tickets.
2014: The Year in Music [PHOTOS]