The DoJ accuses VW of obstruction of justice, allegedly destroying documents related to the scheme.
Then, in May 2006, when VW was devising the EA-189 2.0-litre diesel engine - the cornerstone of a project to sell "clean diesel" cars in the USA - one engineer described the Audi software to a group of employees at the company's brand engine development department, said the new court documents.
VW has already agreed to a $15bn civil settlement with environmental authorities and auto owners in the US.
The U.S. Department of Justice said Wednesday that Heinz-Jakob Neusser, 56; Jens Hadler, 50; Richard Dorenkamp, 68; Bernd Gottweis, 69; Oliver Schmidt, 48; and Jürgen Peter, 59, all of Germany, have been indicted and charged with one count of conspiracy to defraud the United States by a federal grand jury in the Eastern District of MI.
"The knowledge and choices they made went to the executive levels and that did set it apart from other companies", she said at a news conference in Washington.
All of those executives are German nationals and five of them are now in Germany, Lynch said. All are described as heads of divisions or supervisors.
All are believed to be in Germany except for Schmidt, who was arrested in Miami on Friday and appeared in federal court there on Monday.
Lynch said it was "too early to predict" how United States officials might work with their German counterparts to bring the other executives to justice.
A Volkswagen spokesperson declined to comment Wednesday morning.
News of the impending settlement comes as prosecutors move to tie up charges against the German automaker.
Volkswagen said it would also cooperate with inquiries by the Braunschweig and Munich public prosector's offices in Germany.
In a statement, Volkswagen Group CEO Matthias Müller apologized for his company's actions.
The carmaker will plead guilty to three criminal felony counts: conspiracy to defraud the United States and U.S. customers and violate environmental laws; obstructing justice by destroying scandal-related documents; and importing cars using false statements.
"Companies often face the dilemma of whether to protect their employees or cooperate with government investigations, but nearly always end up deciding in the company's best interest to share what information they have", Uhlmann said.
The scandal flared up in 2015 when the US Environmental Protection Agency issued a notice of violation against the automaker.
About 11 million vehicles worldwide were equipped with the software.
A Justice Department spokesman did not immediately respond to a request for comment. Oliver Schmidt, the company's liaison with US environmental regulators, was arrested Saturday in Florida and is scheduled to appear in court there again Thursday. The first was Volkswagen engineer James Liang, who pleaded guilty last September to similar charges. A half dozen senior VW employees have also now been indicted, and the AP reports that upwards of 40 Volkswagen employees sought to cover up evidence of wrongdoing.
The Justice Department settlement with VW will not end the Justice Department's investigation into individual misconduct and more executives may face charges, sources said.
"In the days ahead, we will continue to examine Volkswagen's attempts to mislead consumers and deceive the government".