Winterkorn's indictment brings the US criminal case to the uppermost levels of Volkswagen, which pleaded guilty last year to lying to American environmental regulators about emission control systems.
“If you try to deceive the United States, then you will pay a heavy price,” US Attorney General Jeff Sessions said in a statement.
“The indictment unsealed today alleges that Volkswagen's scheme to cheat its legal requirements went all the way to the top of the company.”
Winterkorn faces four counts, including conspiracy to defraud the United States and wire fraud.
Prosecutors say Winterkorn knew of the company's emissions cheating as early as May 2014 but decided to continue with the fraud, the Justice Department said in a statement.
In the summer of 2015, months before the scandal broke, Winterkorn chaired a “damage table meeting” at Volkswagen's headquarters in Wolfsburg, Germany where engine development staff delivered a presentation on how the company was deceiving US regulators and what consequences the company would face if it were caught, according to the Justice Department.
And following the meeting, Winterkorn authorized the company to continue lying to American authorities.
Winterkorn resigned in September of 2015 following revelations of the company's emissions cheating, in which the company configured as many as 11 million diesel-powered vehicles worldwide, including 600,000 in the United States, to emit up to 40 times the permissible levels of harmful nitrogen oxide but to hide this during testing.
Nine charged, two jailed
A Volkswagen spokesman told AFP the company “continues to cooperate with investigations by the Department of Justice into the conduct of individuals,” but said, “It would not be appropriate to comment on individual cases.”
Eight other individuals have now been charged by US authorities in the scandal. Two VW engineers have been jailed after pleading guilty to participating in the conspiracy.
Winterkorn is charged along with five other Volkswagen executives and employees who were indicted last year, according to court papers. They include senior former engine development and quality managers.
Like Winterkorn, they have not been apprehended and reside in Germany. One former manager of VW's subsidiary Audi AG, Giovanni Pamio, 61, an Italian citizen, has been charged by complaint and currently remains in Germany pending extradition.
The scandal has so far reportedly cost the auto giant as much as $30 billion in criminal fines, class-action settlements and environmental remediation.
A study published in May of last year found that excess nitrogen oxide from improperly configured diesel vehicles had contributed to about 38,000 premature deaths worldwide in 2015.