The four other unnamed Volkswagen executives have all been charged with a variety of fraud charges relating to the scandal.
German prosecutors have charged former Volkswagen CEO Martin Winterkorn and four others with fraud and other offences in connection with the company's massive, multi-year effort to cheat on diesel emissions testing.
Volkswagen admitted in September 2015 to having used illegal engine control software to cheat USA pollution tests, triggering a global backlash against diesel after the scandal that has so far cost the carmaker 29 billion euros ($32.8 billion).
In all, some 11 million cars worldwide were equipped with the illegal software, in a case that damaged the reputation of diesel technology and accelerated the shift to electric cars in Europe.
The charges are the first Winterkorn, 71, has faced in Germany.
They also claim Winterkorn approved a software update, at a cost of €23 million (£19.8 million), that was "useless" but served to "continue obscuring" the use of the defeat device systems.
The software enabled 9m cars, including Volkswagen, Audi and Skoda models, to remain below legal limits for emissions of harmful nitrogen oxides when in test conditions, while continuing to deliver the performance benefits of less stringent standards on the roads.
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Prosecutors admitted "particularly serious" cases of fraud could lead to 10 years in prison.
Even though he knew about the manipulations on diesel engines, Winterkorn had failed to disclose the manipulations either to authorities in Europe and the US or to its customers, according to the public prosecutor.
The prosecutors said they are still investigating 36 more suspects.
They added that this had resulted in Volkswagen being slapped with much higher fines in Germany and the United States than would have been the case had he acted.
Following the court's decision, Winterkorn's lawyer responded that the charges had been brought without giving the former Volkswagen boss the opportunity to "take note of all files of the proceedings" and to comment on them.
The scandal unleashed widespread scrutiny of diesel emissions across the industry.
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