In a separate statement, Daimler confirmed the recall and said the question over the legality of the software would still need to be clarified.
Daimler boss Dieter Zetsche has been summoned to meet transport minister Andreas Scheuer after Germany's KBA motor vehicle authority discovered "inadmissible defeat devices" in Mercedes-Benz engines.
Daimler, like other vehicle manufacturers, uses urea nitrate liquids to naturalize nitrogen oxide emissions in exhaust fumes.
All carmakers use software to manage exhaust emissions filtering and engine performance, but a device can be classified as illegal if exhaust filtering systems are deactivated too early or without good reason.
This morning, Daimler shares were trading 1.76 percent lower, at 61.19 euros, underperforming the Stoxx 600 Automobile index which was 0.48 percent lower.
Daimler said last month it would appeal against an order by the KBA to recall the Mercedes van Vito 1.6l Diesel Euro 6 model, following a transport ministry investigation.
Daimler, like other auto manufacturers, uses urea nitrate liquids to neutralize nitrogen oxide emissions in exhaust fumes.
Since rival Volkswagen admitted in 2015 to cheating USA emissions tests, German carmakers including VW, Daimler and BMW have faced a backlash against diesel technology in which they have invested billions of euros.
Germany can only order the recall of vehicles within its own borders, or of those vehicles issued with a pan-European road-worthiness certification via German authorities.
KBA assumes the devices were meant to help a broad majority of Daimler's new diesel cars pass recently introduced Euro 6 emissions standards.