VW executives also approved a script, "consistent with Winterkorn's alleged directive", for a meeting with CARB to hide their emissions cheating.
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".
Mr Winterkorn is charged with conspiracy to defraud the United States, wire fraud and violating the Clean Air Act from at least May 2006 to November 2015 by using illicit software that allowed VW diesel vehicles to emit excess pollution without detection.
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".
U.S. prosecutors charged Winterkorn with wire fraud and conspiracy to defraud the United States, according to an indictment that was unsealed today. A civil case lodged in 2016 by several states alleged that Winterkorn had been made aware of the illegal software (called a "defeat device" in Environmental Protection Agency parlance) early on at Volkswagen, although at the time he was not personally charged with any wrongdoing.
In the aftermath of revelations about Volkswagen's emissions test cheating, Volkswagen publicly stated that the illegal software had been placed on the cars by "rogue engineers" and that company executives were not involved or culpable. He is the highest-ranking person to be charged in the matter. He went on to say "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 agreed to the plan, the indictment said.
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Volkswagen had initially suggested that only lower-level executives knew of the diesel emissions cheating.
An indictment filed in secret in March, was unsealed on Thursday in U.S. District Court, and names numerous former executives.
A spokeswoman for the US Attorney's Office for the Eastern District of MI in Detroit said Mr Winterkorn was not in custody.
Winterkorn, 70, is believed to be a resident of Germany. Two other employees have pleaded guilty over their role in the affair, and five other executives have been indicted by the United States and remain in Germany, avoiding arrest.
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.