BERLIN-- Volkswagen AG Chief Executive Matthias Müller has been targeted for the first time in a probe in connection with events linked to the disclosure of the company's emissions-cheating scandal, threatening the company's efforts to put the two-year-old saga behind it.

The state's prosecutor in Stuttgart confirmed Wednesday that Mr. Müller, his predecessor Martin Winterkorn, and current Chairman Hans Dieter Poetsch had been under investigation since February on suspicion of stock market manipulation in connection with the scandal.

The Stuttgart probe doesn't allege that the executives are suspected of playing a role in the diesel scandal itself--a conspiracy to mislead regulators about the level of emissions produced by the car maker's diesel engines over several years.

Rather, the Stuttgart probe is looking into whether as members of Porsche SE's board they withheld information from investors about an unfolding U.S. investigation into the manipulation before it became public in 2015, causing Volkswagen's shares to drop and exposing shareholders to big losses.

The revelation is bad news for Volkswagen, which has tried to draw a line under the scandal, in part by handing management to an untainted team led by Mr. Müller. It could also add momentum to thousands of investor lawsuits in Germany that are seeking more than EUR8 billion ($8.9 billion) in damages from Volkswagen and draw the Porsche clan's family holding into the fray for the first time.

Porsche SE manages the 52% stake in Volkswagen AG held by the heirs of Beetle inventor Ferdinand Porsche since sports car maker Porsche AG was folded into Volkswagen in 2012. Volkswagen has pleaded guilty in the U.S. to conspiracy to commit fraud in connection with the emissions cheating and has agreed to pay nearly $25 billion in fines, penalties, legal fees and compensation for customers.

"There is cause to believe that the accused were intentionally late to inform shareholders about the financial consequences, especially for shareholders of Porsche SE, of the software manipulation of diesel vehicles," the Stuttgart state's attorney said in a statement.

A spokesman for Porsche SE said the charge was unfounded and that the company fulfilled its obligations to inform financial markets in a timely fashion. The opening of an investigation by a prosecutor doesn't guarantee that the people affected will be charged, let alone convicted.

Mr. Müller was CEO of sports car maker Porsche AG when the scandal unfolded and a member of the supervisory board of Porsche SE

When U.S. investigators disclosed the scandal on Sept. 18, 2015 and charged Volkswagen with violating U.S. law, the German car maker's shares plunged, losing nearly half their value and causing billions of euros in share losses and causing the company to report its worst ever loss in 2015.

Write to William Boston at william.boston@wsj.com