GE-Free New Zealand says there has been a serious safety breach during a Plant and Food Research trial in Lincoln.
President Claire Bleakley says brassica plants that have been genetically modified have flowered, putting nearby non-modified crops at risk of cross-pollination.
Ms Bleakley says the brassica plants have been modified using insecticides harmful to humans.
She says the breach is a direct violation of controls set out by the Environmental Risk Management Authority and threatens exporters' GE-free promise.
Plant and Food Research spokesperson Bruce Campbell says a safety breach has occurred, but it is unlikely to pose any significant threat to nearby crops.
Mr Campbell says Plant and Food Reseach is taking the mistake very seriously but does not believe it will harm nearby crops.
He says the Ministry of Agriculture and Forestry is investigating the trial.