That contradicted his claim that he didn't learn about it until shortly before U.S. investigators announced it in September 2015. Winterkorn resigned as CEO five days later.
VW has admitted installing software in its diesel cars that turned on pollution controls when vehicles were being tested and switched them off during everyday driving. That made it look as if the cars met tough U.S. limits on harmful pollutants known as nitrogen oxides.
In all, some 11 million cars worldwide were equipped with the illegal software.
Prosecutors said the defendants — all top Volkswagen managers — were part of a deception that started in 2006.
The 71-year-old Winterkorn and the others, whose names were not released, face six months to 10 years in prison if convicted of aggravated fraud involving serious losses. Other charges include unfair competition and breach of trust.
Prosecutors said the defendants could also be forced to forfeit sales bonuses ranging from around 300,000 euros to 11 million euros ($340,000 to $12.45 million).
Winterkorn is already under indictment in the U.S. on charges of fraud and conspiracy to violate the Clean Air Act and could get up to 20 years in prison. But he cannot be extradited from Germany to the U.S.
Winterkorn's attorney, Felix Doerr, said that the defense could not comment on the German case because prosecutors had not provided adequate opportunity to review the case files. Doerr said prosecutors turned over seven DVDs with hundreds of file folders of material on April 5.
The case, consisting of a 692-page indictment backed by 300 file volumes holding 75,000 pages, was filed in a local court in Braunschweig on Friday. The court will decide if the case will proceed to trial.
Prosecutors said among other things that the defendants carried out a software update costing 23 million euros in 2014 to try to cover up the true reason for the elevated pollution during driving.
The prosecutors said they are still investigating 36 more suspects.
Volkswagen's corporate involvement in the Braunschweig investigation ended last year with a 1 billion euro fine. Volkswagen noted that the indictment was against individuals and had no further comment.
The prosecutors' move is only one of the legal proceedings unleashed by the scandal.
Volkswagen has paid more than 27 billion euros (currently $31 billion) in fines and civil settlements with authorities and car owners since getting caught.
The automaker apologized and pleaded guilty to criminal charges in the United States, where two executives were sentenced to prison and six others charged, although they could not be extradited.
And the U.S. Securities and Exchange Commission charged the company and Winterkorn on March 15 with defrauding investors through misleading statements about vehicle quality and environmental compliance.
Investors in Germany are also seeking damages.
The scandal unleashed widespread scrutiny of diesel emissions across the industry. It soon turned out that many models from other companies also emitted far more pollution on the road than on the test stand, because of regulatory loopholes exploited by carmakers such as turning exhaust controls off at certain temperatures to reduce engine wear.
Diesel sales, once half the European car market, have sagged.
That in turn has undermined carmakers' plans to use diesels — which get better mileage — to help meet tougher European Union limits in 2021 on emissions of carbon dioxide, the main greenhouse gas blamed for global warming.
One result has been greater pressure to develop battery-powered cars to avoid heavy fines for breaching the new emissions limits. Volkswagen plans to spend 30 billion euros to develop electric vehicles by 2023.
The company was able to weather the scandal well enough to take the top spot as the world's largest carmaker from Toyota. Last year, under CEO Herbert Diess, Volkswagen had record sales of 10.83 million vehicles, making an operating profit of 13.9 billion euros.
