Volkswagen admitted to cheating emissions regulations in various markets, including the U.S., on a number of its diesel vehicles.
According to the indictment, Winterkorn was briefed in 2015 about the situation, at which time he allegedly gave the green light to continued concealment of the vehicles' defeat devices, which were used to bypass federal emissions regulations.
In May, a VW Executive sent a memo to Winterkorn explaining the situation which stated, "a thorough explanation for the dramatic increase in NOx emissions can not be given to the authorities". It is unclear, however, if German prosecutors are pursuing a parallel investigation that could lead to charges in the disgraced executive's home country.
Volkswagen did not immediately comment.
"The indictment unsealed today alleges that Volkswagen's scheme to cheat its legal requirements went all the way to the top of the company", said Attorney General Jeff Sessions in a written statement. He is the ninth person charged by the U.S. government in this scandal.
The indictment was unsealed in Detroit on Thursday, revealing that Winterkorn had been charged on March 14 with wire fraud and conspiracy to defraud VW's American customers and violate the Clean Air Act.
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Volkswagen's new CEO, Herbert Diess, pledged earlier Thursday that the German manufacturer would step up compliance systems to prevent the sort of misconduct that set off the deepest crisis in the company's history.
The indictment describes a July 27, 2015 meeting at which Volkswagen employees presented PowerPoint slides to Winterkorn and "other senior VW AG management at an in-person meeting at VW's headquarters in Wolfsburg".
The indictment charges that Winterkorn then instructed Schmidt and another VW employee to continue to deceive United States regulators at a follow-up meeting in August, "using excuses such as "irregularities" and "abnormalities" for the discrepancy".
The indictment also states that Winterkorn was informed of the emissions cheating by a memo sent in May 2014.
VW had initially suggested that only lower-level executives knew of the cheating.
A spokeswoman for the US Attorney's Office for the Eastern District of MI in Detroit said Mr Winterkorn was not in custody. Two VW engineers have been jailed after pleading guilty to participating in the conspiracy. One former manager of VW's subsidiary Audi AG, Giovanni Pamio, 61, an Italian citizen, has been charged by complaint and now remains in Germany pending extradition.
The September 2015 disclosure that VW had for at least six years intentionally cheated on emissions tests did massive damage to the company's reputation around the world and prompted massive compensation and vehicle refit costs.