Audi later confirmed the raids, saying in a statement that it would "fully cooperate" with the authorities.
VW, Audi's parent company, has drawn criticism amid the so-called Dieselgate scandal, details of which revealed that up to 11m of the auto giant's vehicles worldwide had software installed that cheats emissions tests.
The US government and VW have agreed on a so-called statement of facts recently, including accusations that Audi engineers designed a 3.0 liter diesel engine for the American market equipped with a so-called defeat device created to mislead authorities and customers on emissions.
The searches were carried out in order to identify those involved in installing the devices that cheated the diesel tests, Munich prosecutors said.
The raid also coincided with a major annual press release conference at which Stadler was presenting Audi's 2016 earnings.
A statement from the prosecutor on Wednesday's raids cited suspicion that the cars, sold in the United States between 2009 and 2015, were also fitted with devices to cheat tests.
Volkswagen's headquarters in Wolfsburg were not spared of the search, and investigators also checked six other unspecified facilities.
Volkswagen shares were marked 1.57% lower by mid-day in Frankfurt and changing hands at €139.77 each, although the stock has risen some 40% since hitting an all-time low in early October 2015 after news of the emissions scandal first broke. Audi declined to comment on the probe. Protecting profit at Audi, its biggest earnings contributor, is key for VW Group as it spends money on fixing as many as 11 million rigged diesel cars while maintaining financial firepower to develop electric models and new digital services.
Audi boss Rupert Stadler was accused of involvement by a former employee, but the luxury carmaker's board reiterated their conference in him in late February. However, German prosecutors said they were not investigating specific Audi managers, with the charges leveled at persons unknown so far.