In a statement, Audi said it was co-operating with authorities.
Prosecutors in Munich have always been investigating whether the Volkswagen subsidiary could also be held responsible for the so-called Dieselgate scandal that erupted in 2015, when it emerged that 11 million cars worldwide had been equipped with software to deceive emissions tests.
"The execution of the search warrants is meant to clarify which persons were involved in the use of the relevant technology and, where applicable, were involved in providing inaccurate information to third parties", Heidenreich said in a statement.
Munich prosecutors searched the Audi offices in the southern state of Bavaria shortly before the auto group's chief Rupert Stadler presided over the premium carmaker's annual press conference, a company spokesman said.
"I have all along supported efforts to clear up the diesel issue at Audi", he told reporters, while conceding that efforts to recover from the scandal were "far from over".
German prosecutors have raided Audi and VW sites as part of a probe into the manipulation of USA emissions tests.
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VW's Wolfsburg headquarters were searched, along with Audi's Ingolstadt and Neckarsulm factories and six other unspecified sites, the group said.
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. Audi declined to comment on the probe.
Also, finance chief Axel Strotbek said he now did not expect the need to further increase provisions for Dieselgate beyond the 1.63 billion euros ($1.73 billion) Audi has set aside so far.
The raid at Audi's sites coincided with the company's annual press conference, in which it reported pre-tax profits of 3bn euros (£2.6bn) for 2016, a 37% drop on the previous year.
The raids are the first at Audi since VW's diesel scandal broke 18 months ago.
More than two million Audis had the manipulated software, including more than half a million in Germany alone.