"The accused are suspected of knowingly delaying telling shareholders about the financial consequences for Porsche SE of software manipulation in diesel vehicles by Volkswagen AG," the prosecutors in southwestern city Stuttgart said.
Holding company Porsche SE - separate from VW subsidiary Porsche AG - owns a controlling stake in the world's largest carmaker, with its stable of 12 brands ranging from luxury Audi to generalist Skoda.
Along with Müller, former VW CEO Martin Winterkorn and Porsche SE chairman Hans-Dieter Poetsch are also suspected of failing to share information about the emissions cheating affecting 11 million cars revealed in 2015.
Investigators opened the dossier in February, in response to charges levelled by German financial supervisor BaFin in summer 2016.
It is the first time Müller has been targeted by prosecutors over market manipulation, while Winterkorn, Poetsch - a former chief financial officer at VW - and VW brand chief Herbert Diess already face probes.
Volkswagen faces an array of legal challenges in Germany and worldwide relating to its software, designed to fool regulatory nitrogen oxide emissions tests.
Shareholders and car buyers have launched suits seeking compensation, while prosecutors in Brunswick, north Germany, are investigating 37 individuals at the company for fraud.
Others face probes over incorrect carbon dioxide emissions data.
The gigantic carmaker has so far set aside more than €22 billion to cover fines and compensation related to the "dieselgate" affair, but experts estimate the final bill could be much higher.