Monsanto says it will appeal a court order to destroy genetically modified sugar beet seed stock.
This ruling is the second setback for users of herbicide resistant sugar beets.
Earlier this year the same federal judge ruled the U.S. Agriculture Department approved use of the Roundup Ready beets without proper environmental review.
More than 90 percent of sugar beets planted in Minnesota and North Dakota this year were the genetically modified variety.
Industry experts say the legal dispute could lead to a shortage of high quality non-genetically modified seed.
There could also be a shortage of chemicals to control weeds if farmers can't plant the herbicide resistant variety.
Minnesota and North Dakota make up the largest sugar beet producing region in the country.