The EU currently applies a zero-tolerance policy for non-approved genetically modified organisms (GMOs) in food and feed imports.
According to the Commission report, most of these GMOs have suffered delays in the approval system but have received regulatory approval in countries outside the EU or have a positive safety assessment from the European Food Safety Authority (EFSA).
Because of the differences in the GMO authorisation regimes between the EU and exporting countries, conflicting authorisations of GMOs have occurred.
Codex said these could become more frequent and affect a greater range of crops in the future.
Codex establishes food standards, ensures fair trade practices in the food trade and promotes the coordination of all food standards work undertaken by international organisations on behalf of the UN's Food and Agriculture Organisation and World Health Organisation.
It has decided to advance a proposal that addresses the risk assessment of low-level presence of biotech plant materials, found in food or feed, which have been authorised in one or more countries but not yet in the importing country.
This decision followed negotiations by members of the Codex ad hoc Task Force last week in Chilba, Japan.
Codex's proposal will be submitted to the Codex Commission next July for approval, and will subsequently be incorporated in the Codex Plant Guidelines as an annex including information-sharing mechanisms.
This system would not substitute the full food safety assessments under the Codex Guidelines for products to be marketed in an importing country.
It will also not address risk management measures, so individual countries will need to decide when and how to use the guidelines within the context of their regulatory systems.
No country would be obliged to adopt the document.
Codex's decision has been welcomed by European industry representatives, according to EuropaBio, the European Association for Bioindustries.
"The delays in approval of biotech products in Europe compared to the rest of the world as well the absence of a science-based approach to address low level presence is already leading to trade disruption and seriously impacting the supply of feedstuffs," said Johan Vanhemelrijck, secretary general of EuropaBio.
"Moreover, this unresolved issue that bears no relationship with safety is having a damaging effect on public confidence towards biotech products.
In light of the Codex decisions, we hope that the EU will revisit its zero tolerance policy towards low level presence, speed up its approval process and define the appropriate science-based approach so that European food and feed supplies are secured."
Europabio says this issue should be addressed in a globally consistent way to ensure that all countries have an equal opportunity to trade food and feed materials freely with one another.
However, some have criticised Codex's proposals, disagreeing with only applying regulations to new foods merely because a certain technique has been used.
Henry Miller, a delegate to the task force in Japan, wrote in The Washington Times: "It is one thing to regulate new foods with traits that are of potential concern, but quite another to regulate new foods merely because a certain technique has been used, especially when that technique is state-of-the-art and superior to its predecessors… Virtually everything in our diets has been genetically improved by one technique or another." Organisations such as Greenpeace and Friends of the Earth are entirely against genetic modification.
Clare Oxborrow from Friends of the Earth told FoodNavigator: "We are concerned by attempts to legalise contamination of unapproved GM ingredients through Codex.
The GM industry has failed to control contamination of the food chain, as last years GM rice contamination incident highlighted.
"It is outrageous that instead of tightening up controls to prevent this contamination happening in the first place, the US is attempting to legalise such contamination.
Governments must uphold European legislation which has a zero tolerance approach to unauthorised GMOs to ensure that consumers and the environment are protected."
GM crops are increasingly cultivated in major crop exporting countries.
The adoption rate of cultivating GM crops has seen double-digit annual growth since 1996.
In 2006, 10.3m farmers in 22 countries cultivated biotech crops on 102m hectares.
Ninety per cent of farmers who benefited from these crops were from developing countries, according to the commission's study.