Investigators say they have "sufficient indications" that Winterkorn may have known earlier than he has so far admitted about the cheating, adding his and 15 other names to a growing list of people facing probes for fraud and false advertising.
Winterkorn is already under investigation for suspected market manipulation related to the scandal.
The new evidence comes from "questioning of witnesses and suspects and the examination of confiscated computer files," the prosecutor's office in the north German city of Brunswick said in a statement.
With the 16 names added Friday, there are now a total of 37 people under investigation.
Prosecutors added that they have this week searched 28 homes and offices linked to the new names on the list, and will take several weeks to evaluate the materials they seized.
Volkswagen admitted in September 2015 to installing so-called "defeat devices" in 11 million vehicles worldwide, after their existence was revealed by the US Environmental Protection Agency.
The software caused engines to reduce emissions of harmful nitrogen oxide when they were undergoing regulators' tests.
Winterkorn - known inside VW as "Mr Quality" for his perfectionism - stepped down the same month, but has always denied any knowledge of the cheating before it became public.
US investigators and German media have alleged that VW executives knew of the scandal as far back as July 2015, but decided to say nothing.
"That is not the case," Winterkorn told German lawmakers at a parliamentary hearing into the dieselgate affair earlier this month.
VW agreed this month to plead guilty to fraud and pay fines amounting to $4.3 billion (€4.0 billion) in the United States to close its emissions cases with the Department of Justice.
The payment, which will allow VW to avoid a trial, comes on top of $17.5 billion in fines and compensation already agreed to cover the costs of the scandal in the US.