"I am shocked by the events of the past few days. Above all, I am stunned that misconduct on such a scale was possible in the Volkswagen Group," Winterkorn, 68, said in a statement.
"Volkswagen needs a fresh start -- also in terms of personnel. I am clearing the way for this fresh start with my resignation," he said.
Earlier, the German government launched an investigation into the allegations that the the world's second-largest auto maker manipulated data on pollution control tests.
An inquiry commission set up by the government to investigate the charges against the iconic German auto giant will take up its work by visiting Volkswagen's headquarters in Wolfsburg in the state of Lower Saxony this week, federal transport minister Alexander Dobrindt announced.
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The commission chaired by state secretary in the transport ministry Michael Odenwald will examine among other things whether the concerned cars were built and tested in conformity with existing German and European guidelines and whether they fulfilled the requirements of Germany's Technical Inspection Agency, which issues the road worthiness certificate for automobiles, Dobrindt told a news conference yesterday.
A special software enabled the cars to detect when they were undergoing emissions control tests and to lower their pollution levels.
It could hide the fact that the emission levels of diesel cars were 40 times higher than the level of pollutants allowed in the US.