Daniel Donovan says in a whistleblower case that he was wrongfully fired December 6, 2015 after refusing to participate in the deletions and reporting them to a supervisor.
The lawsuit says that the evidence deletion continued for three days after the September 18 allegations from the EPA and despite a hold order from the Justice Department.
VW has admitted that it programmed about 600,000 diesel-powered cars in the US to turn on pollution controls during EPA treadmill tests and turn them off when the cars were on the road.
The Justice Department is investigating potential criminal charges against VW, and the company has been negotiating with the EPA and California regulators to come up with repairs.
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VW faces a March 24 deadline from a federal judge to reach agreement on the fixes.
Donovan worked as a technology employee with VW's general counsel office who was responsible for electronic information management in injury and product liability cases.
The lawsuit said he was fired "because of his refusal to participate in a course of action that would spoilate evidence and obstruct justice" in the EPA and Justice Department probes.
"We believe his claim of wrongful termination is without merit," the company said today in a statement.
Donovan, who worked in VW's Michigan offices, alleges that the company's information technology department did not stop deleting items until September 21, so Donovan reported his concerns to his supervisor, according to the March 8 lawsuit filed with the Oakland County Circuit Court in Pontiac, Michigan.
It also says the department was not preserving backup disks.
Donovan was fired because VW of America believed he was about to report the deletions and obstruction of justice to the EPA, Justice Department or the FBI, according to the complaint.