The judgement follows legal action by a German beekeeper who sought compensation from the Bavarian government after he was prevented from selling his honey because it contained traces of GM pollen.
The ruling, which comforted the plaintiff, could pave the way for compensation claims by beekeepers against biotech companies such as Monsanto or governments which authorise test fields.
An EU spokesman said the ruling could hit imports of honey from countries like Argentina, where GM crops are widely grown.
Monsanto stressed that there were no safety concerns regarding its MON 810 maize and said the case was about the legal technicalities of EU approvals of the specific maize variety.
The variety was approved for cultivation in the EU in 1998.
Asking for compensation
The beekeeper, in his demand for compensation from the Bavarian authorities, said the pollen was contaminated by government field trials of Monsanto's 810 maize variety, which took place some 500 metres from his hives.
In November 2009 the Bavarian Higher Administrative Court forwarded the case and a number of related questions to the ECJ for a ruling.
The court endorsed its Advocate-General's February 2011 opinion, which noted that honey containing pollen from Monsanto's MON 810 maize is not covered by an authorisation issued under the EU regulation on genetically-modified food.
Additionally the Advocate-General concluded that "food containing material from a genetically-modified plant, whether that material is included intentionally or not, must always be regarded as food produced from a GMO".
Call for zero tolerance
Environmental NGOs and the Greens in the European Parliament hailed the ruling as a victory for beekeepers, consumers and the European GM-free agriculture movement.
The Greens said that the ruling "directly challenges" the abandonment of EU zero-tolerance rules for unauthorised GM contamination.
Greenpeace EU's agriculture policy adviser Stefanie Hundsdorfer further argued that the ECJ ruling "highlights how conventional and genetically-modified agriculture cannot co-exist. When a GM crop is grown in open fields, contamination is impossible to stop".
Her comments were echoed by French Green MEP José Bové, who described the case as "proof that co-existence is a fallacy and that GM cultivation does not leave a choice for GM-free products".
For Friends of the Earth Europe's food campaigner Mute Schimpf, yesterday's ruling "re-writes the rule book and gives legal backing to stronger measures to prevent contamination" from GM crops.
The European Commission sought to regulate the co-existence of GMOs with other crops in a 2010 recommendation, which is not legally binding. The recommendation was part of a wider package which proposed allowing individual EU member states to ban GMO cultivation on their territory.
Discussions on adopting the new rules are still ongoing.
"When co-existence measures are not sufficient to prevent the unintended presence of GMOs in conventional or organic crops, member states may restrict GMO cultivation in large areas of their territory," the Commission said.