The decision has dealt a serious blow to the biotechnology industry and in particular to Bayer Cropscience, the manufacturer of the GM variety. Two other Bayer-produced GM rape varieties are awaiting approval by German regulators.
The Belgian ruling will now be reviewed by other EU Member States, though it is expected that they will back the decision. As officials point out, the ruling is backed by the conclusions of one of the world's largest scientific studies into the impact of GM crops on the environment. The UK's farm-scale trials suggested that growing GM spring-sown rape and sugar beet were more damaging to wildlife such as insects, though GM maize was less harmful.
Anti-GM pressure groups such as the UK-based Friends of the Earth (FoE) believe that governments should not be rushing into the cultivation of oilseed rape. There have been cases in North America where this has led to the contamination of non-Gm farmland.
"The fact is that oil seed rape is a very small seed, and can easily be blown around," said FoE campaigner Pete Riley. "The pollen can spread several kilometres. This means that genetically modified seeds are easily blown onto non-GM farmland, and these 'volunteer' crops, as they are called, are finding their way into our food chain whether we like it or not."
But to complicate matters further, the European Commission has warned that it might challenge member-state bans on biotech crops in the European Court of Justice. Bans have also been imposed by Austria, France, Germany, Greece, Italy, Luxembourg and the UK.
While farmers can group together voluntarily into biotech-free zones, the commission said in a seven-page document on food biotechnology that it would act against any national or regional laws preventing coexistence of biotech and conventional crops.
Bayer now has the right to appeal to the Belgian courts to have the decision overturned. Belgian ministers have already given the go-ahead for the GM rape variety to be imported from outside the EU and processed, since this would have no environmental impact.
The biotechnology industry will be looking closely at this case. It would no doubt regard a final decision to prevent it from marketing spring-sown rape for cultivation in the EU as a serious setback.
However it regards the future of winter-sown GM variants as far more important to their commercial success since these would be used over much greater areas across Europe.