Justice Denis Clifford ordered in the High Court in Wellington on Friday that any decisions to accept applications be set aside and Erma stop hearing and assessing any further applications
GE-Free had taken both Erma and AgResearch to court in March.
AgResearch last year made four applications for the laboratory testing of human and monkey cell lines and smaller species of genetically engineered laboratory animals and the development of GE cows, buffalo, sheep, pigs, goats, llamas, alpacas, deer and horses.
It wanted the livestock to produce antigens, biopharmaceuticals, enzymes, hormones and other products with possible health benefits and commercial applications.
AgResearch said it was making a "suite" of applications to obtain all the possible approvals it might need for research, and animal breeding to target production of high-value proteins in milk.
But GE-Free said Erma had wrongly allowed the applications to go ahead, because too little information had been provided on the new organisms to be created or where they would be developed and tested.
The public and farmers were against the "wholesale approach to genetic engineering of animals", he told NZPA.