Volkswagen said the issue, which it came across while investigating diesel emissions, could cost about €2 billion.
Brands including VW, Audi, Skoda and Seat could be affected.
The issue mainly affects diesels, but could also include petrol models.
CO2 is a greenhouse gas, as opposed to the NOx involved in earlier allegations, which is a pollutant that causes lung disease.
The so-called irregularities that have now been found relate to the way in which CO2 emissions and fuel consumption were measured during the technical approval process for some models.
VW has not said whether or not it believes those irregularities were caused by deliberate action and it also has not specified which models are affected.
The company’s CEO Matthias Muller said: “From the very start I have pushed hard for the relentless and comprehensive clarification of events. We will stop at nothing and nobody. This is a painful process, but it is our only alternative. For us, the only thing that counts is the truth.”
The company’s board will talk to regulators about the consequences of its discovery, VW said in a statement, adding that “the safety of the vehicles is in no way compromised”.
The supervisory board issued a separate statement saying it was “deeply concerned” and promising “to ensure swift and meticulous clarification”.
The latest setback comes a day after US authorities accused VW of fitting nitrogen oxide defeat devices on its larger 3.0 liter diesel vehicles – charges which VW denied.
VW is already beset by scandal after the EPA discovered that some of its diesel vehicles were fitted with software that detected when they were undergoing emissions tests and changed the way they operated.
The so-called defeat device is understood to be in 11 million vehicles worldwide.
Earlier, it was announced that VW’s sales in the US had risen in October, despite the scandal.
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