Judy Kinderlerer, a food microbiologist at Sheffield Hallam University, has been awarded a pounds 35,000 government grant to investigate the problem, which costs manufacturers millions of pounds.
Most manufacturers believe the unsightly speckles are nothing more sinister than crystallised cocoa butter fat.
But Ms Kinderlerer thinks the speckling is caused by a fungus, Chrysosporium farinicola, which reaches cocoa beans from the soil of the tropical countries where they grow and survives the roasting, manufacturing and packaging process.
She said: 'Chrysosporium farinicola is an odd fungus which can grow in very dry conditions, in oxygen-free packaging, in high fat, in high temperatures and in foods with a high sugar content. We aren't sure yet whether or not the fungus is harmful. That will form part of my study.'
Her study involves buying chocolate at random, letting it go mouldy in controlled conditions and isolating the different types of mould that develop.
One leading manufacturer lost pounds 2.5m when a large quantity of chocolate was badly affected by speckling and dumped.