The charges contradict the German carmaker's steadfast insistence that no members of its management board were involved in the emissions fraud.
Thus far, the scandal has cost the company more than $30 billion in buybacks and fines, with more likely on the way in Germany. At the time, USA regulators threatened to withhold authorization for Volkswagen to sell 2016 model year vehicles in the United States until the company explained the discrepancies raised by the ICCT study.
The indictment also alleges that VW employees recommended the company seek to get approval for 2016 diesel models from USA regulators without revealing the existence of the cheating software.
Martin Winterkorn was indicted on four counts of conspiracy and wire fraud, becoming the most senior VW executive to be charged in connection with the scandal.
The indictment, filed in secret in March, was unsealed in US District Court on Thursday as Volkswagen held its annual meeting in Germany.
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The charges stem from the VW Group diesel emissions scandal that broke in 2015.
In March a year ago, VW paid a $2.8 billion fine after pleading guilty to deceiving USA regulators with the defeat devices.
Eight other individuals have now been charged by U.S. authorities in the scandal. All men are German citizens and are believed to be in Germany.
A spokeswoman for the USA attorney's office in Detroit said Winterkorn is not in custody. In total, nine people have been charged and two former Volkswagen executives have pleaded guilty in the case and been sentenced to prison terms.
Volkswagen pleaded guilty a year ago to cheating on emissions tests by using software in almost 600,000 of its diesel vehicles in the USA and agreed to pay $4.3 billion in penalties. 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 scheme came undone when a company employee, in response to a regulator's questions, admitted that VW had been using software to cheat on emissions tests.
Winterkorn is the highest-ranking VW official to be charged in the USA for his role in the cover-up.
"We must prevent that the claims of the victims of the VW diesel scandal become invalid because the limitation period has run out".