The penalty is the largest against an automaker in U.S. history.
The government also said a grand jury has returned an indictment against six VW executives and employees for their roles in the scheme.
The deal announced Wednesday also requires VW to cooperate in an ongoing probe that could lead to the arrest of more employees.
Government documents accuse six VW supervisors of lying to environmental regulators or destroying computer files containing evidence.
VW admitted programming diesel engines to turn on pollution controls during government tests and switch them off in real-world driving. .
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