Katherine farmer Jess Bishop said the order would cost him tens of thousands of dollars and potentially ruin his reputation, in what was his first season as a farmer.
Mr Bishop grew cavalcade and sorghum as part of a share-cropping arrangement on Scott Creek Station, south-west of Katherine.
A visit by officers from the Weeds Management Branch in May confirmed the presence of the weeds grader grass, sicklepod and sida in hay bales on Scott Creek Station.
After protracted negotiations, Mr Bishop was issued with an order to “clean or treat” the remaining hay bales at the pelleting plant in Katherine.
“The order that I have says all hay must go the the pelleting plant, which is a big problem because I still have 1,240 bales of sorghum [hay] that were never contracted to [the pelleting plant],” Mr Bishop said.
Read more of the news story here