The Volkswagen emissions scandal reached the highest echelons of the company on Thursday after its former chief executive was charged with conspiracy in the company’s rigging of diesel vehicles to feign compliance with federal pollution standards.

The indictment of the former executive, Martin Winterkorn, who resigned shortly after the emissions scandal erupted in September 2015, significantly raises the stakes for Volkswagen.

The charges contradict the German carmaker’s steadfast insistence that no members of its management board were involved in the emissions fraud. They also weaken the company’s defense in a related suit by shareholders — potentially adding billions of dollars to the scandal’s already astronomical cost.

Despite President Trump’s efforts to water down auto emissions standards, the indictment indicates that the Justice Department continues to pursue an investigation of Volkswagen that began during the Obama administration. And it provides a rare spectacle: a chief executive facing criminal charges.