The federal government argued that the suit was moot because the Fish and Wildlife Service has already agreed to stop the practice after this year.
But in a ruling Tuesday, U.S. District Judge James E. Boasberg rejected that argument. He set a hearing for Nov. 5 to determine appropriate remedies.
In their lawsuit last year, the Center for Food Safety and two other groups argued that the Fish and Wildlife Service violated environmental laws in allowing the genetically modified crops, mostly corn and soybean. They claimed the practice has harmful environmental impacts.