Since the scandal broke, the company’s chief executive, Martin Winterkorn, has resigned, nine employees have been suspended, and the company has begun the twin tasks of designing fixes for the vehicles and containing consumer outrage and litigation. The Justice Department’s suit and its accusation of continuing obstruction were fresh blows to its new chief executive, Matthias Müller, and will make damage control more difficult.

In a statement, Volkswagen, which includes the brands Audi, Porsche and Lamborghini, said it “will continue to work cooperatively with the E.P.A. on developing remedies” to bring its diesel vehicles “into full compliance with regulations as soon as possible.” The company also said it was working “to develop an independent, fair and swift process for resolving private consumer claims relating to these issues.”

Regulators across the globe, including in India, South Korea and Germany, are conducting their own investigations, as are attorneys general in all 50 states. But the Justice Department has been seen as the only agency that might hold executives personally accountable.

“With today’s filing, we take an important step to protect public health by seeking to hold Volkswagen accountable for any unlawful air pollution, setting us on a path to resolution,” said Cynthia Giles, assistant administrator for the Environmental Protection Agency’s Office of Enforcement and Compliance Assurance. “So far, recall discussions with the company have not produced an acceptable way forward. These discussions will continue in parallel with the federal court action.”