The car giant, which is already mired in scandal for cheating on nitrogen oxide emissions tests, may face further costs of £1.4bn.
Volkswagen says it has found “inconsistencies” in carbon dioxide emission levels which could affect around 800,000 cars.
The German car giant said the “unexplained” anomalies found by an internal probe raised a new problem that could cost it around €2bn (£1.4bn).
It has already been badly hit by the discovery that it cheated on US tests for nitrogen oxide emissions in diesel engines. It is thought that 11 million cars worldwide have been affected, including almost 1.2 million in the UK.
Last week the company reported a quarterly loss for the first time in at least 15 years after setting aside €6.7bn (£4.8bn) to cover the costs of the scandal – even before taking into account penalties, fines or compensation.
VW did not identify the vehicles affected by the latest discovery but said the flaw did not compromise their safety. It was not clear whether the 800,000 were among those already affected by the nitrogen oxide scandal.
It did say the new number was predominantly comprised of vehicles with diesel engines.
Chief executive Matthias Mueller, who took over as VW boss in the wake of the wider scandal which emerged in September, said the company would “relentlessly and completely clarify what has happened”.
Transport Secretary Patrick McLoughlin last week told MPs that the German firm had “acted disgracefully”.
He agreed Volkswagen should face the “full financial implications”, raising the prospect that it could face a £600m bill to compensate motorists who have seen the re-sale value of their cars reduced.
In the UK, the firm is preparing to recall and fix 508,000 Volkswagen cars, 390,000 Audis, 132,000 Skodas, 80,000 VW commercial vehicles and 77,000 Seats, with the process expected to begin in the new year.