Audi was responsible for designing and manufacturing some of the engines that enabled the Volkswagen to cheat on emissions tests.
Audi-owner VW has already agreed to settlements of $21bn (£17bn) in the US.
As a reference, the controversy over Volkswagen erupted in September 2015, when it turned out that the company illegally equipped its cars with a software that underestimated the true level of emissions of harmful substances.
Evidently, reporters who were present at the event asked the company's CEO about the situation, and Stadler's reply was that he "has always supported efforts to clarify the diesel issue at Audi".
The search included VW's Wolfsburg headquarters, along with Audi's Ingolstadt and Neckarsulm factories and six other unspecified sites, the group said.
Volkswagen has issued a global recall of all vehicles affected by the diesel manipulation and has pleaded guilty to conspiracy to commit fraud in the US, agreeing to pay fines, penalties and consumer compensation of around $25 billion.
Unlike the situation with VW, the investigation that sent prosecutors to the offices of Audi was focused on the 3.0-liter V6 TDI engines that were used in its luxury models.
Peter Mertens, senior vice president for R&D at Volvo Car Corporation, will take up his position as head of technical development at Audi on May 1, the CEO said, replacing former R&D boss Stefan Knirsch, who left the manufacturer in connection with the emissions scandal.
Cars sold in European markets are outside the scope of the investigation, the prosecutor said. "We will keep at it".
Audi's two biggest plants were searched by German prosecutors today while its chief exec was announcing the vehicle giant's earnings at its annual press conference today.
Stadler said his private home was not searched in the raid.
"The path towards clearing up (the emissions scandal) is far from over", Stadler said on Wednesday at the carmaker's earnings press conference. Audi's deliveries in China fell 5.8 percent to 32,155 cars last month.