The investigation relates to some 80,000 vehicles fitted with Audi 3.0-litre V6 diesel engines sold in the United States.
Investigators from Bavaria, Baden-Wuerttemberg and Lower Saxony states searched "sites belonging to Audi AG and seven other locations" on suspicion of "fraud and illegal advertising", Munich prosecutors said in a statement.
The investigation relates to some 80,000 vehicles fitted with Audi 3.0-litre V6 diesel engines sold in the United States between 2009 and 2015, prosecutors said.
"There is suspicion that devices were built into these vehicles to manipulate emissions readings and conform to US emissions limits, without the buyers being informed," they continued.
"Prosecutors from Munich and Stuttgart searched offices at our sites in Ingolstadt and Neckarsulm," an Audi spokesman confirmed to AFP, adding that "we are cooperating fully with the authorities."
Audi parent Volkswagen admitted in late 2015 to installing so-called "defeat devices" into 11 million diesel vehicles worldwide, designed to reduce emissions of harmful nitrogen oxides when engines were undergoing regulatory tests.
Most of the affected cars fall under the VW brand, but vehicles made by the group's Audi, Skoda and Seat brands were also among those carrying the software.
With the searches, investigators hope to uncover "which people were involved in the application of the technology and possibly in providing incorrect information to third parties," the prosecutors' statement read.
Two top engineers at Audi stepped down in the space of a year over the scandal, most recently head of technical development Stefan Knirsch in September.
VW has so far set aside more than 22 billion euros ($23.4 billion) to cover fines and compensation related to the "dieselgate" affair, but experts estimate the final bill could be much higher.
Meanwhile, investigations in several countries are seeking to establish who at the group was responsible for the cheating.
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.
"There is still a long way to go before (dieselgate) is finally cleared up," Stadler told journalists at the firm's annual results press conference Wednesday. "We will keep at it."