Setting the threshold of 'unavoidable' traces of GM seeds in other products - how much GM material may be tolerated without labelling in batches of conventional seed - has led to heated discussions at both national and European levels with environmental groups pushing for zero tolerance.
There are fears that allowing GM seeds will lead to a contamination of the food chain that will be difficult to control by farmers and food makers.
"The Commission must take into account the reality that most European farmers, processors and retailers have to supply a non-GMO market," said Stefano Masini of Italy's Coldiretti, Europe's biggest farmer association.
A threshold above the detection limit will burden the production process with uncertainty, additional risks and costs. If creeping contamination becomes the rule, the production of non-GM food will become a costly and high-risk business, he added.
But by contrast, Europe's biotech industry will hope the outcome of today's discussions will lead to long-awaited continuity of rules across the EU.
"We have conscientiously been working on clear rules for the industry for more than 5 years - this is an issue that must be addressed," said Simon Barber from Europabio , the industry body that represents European biotech associations and companies.
Last year the Commission came up with a proposal, which Europabio supported, that set the threshold for GM material in seeds at 0.5 per cent. There are now suggestions that this will fall to 0.3 per cent.
"Bringing the level down to 0.3 per cent will be very costly for the industry," Barber said to FoodNavigator.com, adding that while the seed industry cannot produce 0 per cent, extremely low levels are possible, but only at a price.
Also likely to be on the Commission's agenda today is the authorisation of biotech seeds - not approved at an EU level and only by some member states, such as Great Britain and Spain. The EU executive will discuss entering strains of Monsanto's 810 maize into the EU's overall seed directory that includes all national seed catalogues.
Green groups claim that clearing the way for widespread use of GM seeds is irresponsible because most member states do not have any rules in place to guide farmers on how they should separate organic, conventional and genetically modified crops to minimise cross-contamination.