The event, entitled 'Co-existence of genetically modified, conventional and organic crops - Freedom of choice' opens today in Vienna but already it appears that the context of the debate has been called into question.
"It is ironic that a conference that is labelled as freedom of choice does not include any of the thousands of farmers or independent scientists with co-existence experience in the speakers line up," said Simon Barber, director of the plant biotechnology unit at EuropaBio - the European association for bioindustries.
"Furthermore several farmers who requested a platform to speak were denied the opportunity."
Nonetheless, the European Commission is hopeful that the conference, which forms part of the Commissions consultations with interested parties on the development of efficient and cost-effective strategies to ensure co-existence, will achieve real progress.
The Commission says it is keen to hear the views of all stakeholders before drawing any final conclusions.
"This conference is a crucial step in the consultation process," said Mariann Fischer Boel, commissioner for agriculture and rural development.
"We have brought together people of the very highest calibre to cover all aspects of the co-existence issue. Efficient and cost-effective strategies to ensure co-existence are vital to ensure a practical choice between GM and non-GM produce for farmers and consumers.
"This is not a question of health or environmental protection, because no GMOs are allowed on the EU market unless they have been proved to be completely safe. But segregation measures must be in place to ensure that accidental traces of GMOs in conventional or organic products are kept within the strict ranges defined by EU legislation."
But EuropaBio is concerned that the debate has been slanted in favour of those opposing GM crops, and that not every viewpoint will be heard.
"Thousands of European farmers grew GM last year, successfully co-existing with their neighbours - yet they were not invited to present their practical experience," said Barber.
"In the last three years alone, independent, scientific studies on co-existence have been conducted in six European countries yet these scientists with field experience were not invited to present their findings."
The debate comes at a critical time. EU Member States are currently developing national regulatory approaches to co-existence following the EC's adoption of an overview of the state of implementation of national co-existence measures last month.
The Commission believes that dialogue is now essential to decide about the most appropriate way forward on this important issue.
The three-day conference hopes to achieve this by bringing together policy makers, scientists and a broad range of stakeholders, such as farmers and consumers associations, NGOs and seed producers.
Speakers at the event will include Stavros Dimas, commissioner for the environment and Josef Prll, Austrian minister for agriculture, forestry, environment and water management. Three workshops will discuss different national and regional approaches to co-existence, technical and economic aspects of segregation and consumer attitudes and market responses to GMOs.