"There is suspicion that the accused were partly responsible for at least a significant proportion of vehicles introduced into circulation with manipulative exhaust management software," prosecutors in the Bavarian capital said in a statement.
It is the first time that former members of the high-end VW subsidiary's board have been targeted in the "dieselgate" emissions cheating scandal.
German business weekly WirtschaftsWoche reported the two executives were former engineering chief Ulrich Hackenberg, who quit Audi in 2015, and former technical development director Stefan Knirsch, who left in 2016.
No current members of the Audi board are in prosecutors' sights, the investigators said.
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Audi declined to comment on the raids when contacted by AFP.
The cars with the four-ring logo have figured prominently in the diesel scandal since Volkswagen admitted in 2015 to manipulating exhaust control software in 11 million vehicles worldwide, allowing cars to spew up to 40 times as many harmful emissions on the road as in regulatory tests.
The German investigation focuses on some 210,000 vehicles sold on European and American markets from 2009 onwards.
They bring the total number of searches directed against the carmaker to four over the past year, beginning with a March 2017 raid at its Ingolstadt headquarters.
After two arrests, one former manager in motor development remains in custody while an engineer was released in November.