MAF Biosecurity is considering whether to prosecute the Plant & Food Research Institute after genetically modified plants were found growing outside a containment glasshouse at Lincoln.
The two suspect Arabidopsis thaliana plants belong to a small, widespread weed species commonly used in plant science as a research tool and teaching aid.
The biosecurity agency has issued a compliance order for removal of any other plants, as well as removal or treatment of the soil and a review of procedures at the site.
MAF will inspect the site again next month.
It's the second time Plant & Food, formerly the Crop & Food Institute, has been taken to task for breaching consent conditions.
It was forced to abandon a GM brassica field trial earlier this year after one of the plants was allowed to flower in the open environment at the research site.