The Ensus UK-operated factory at Wilton, Teeside, has been offline since February.
The cuts are due to volatile market conditions across the European bioethanol industry.
After EU legislation changes in April affecting production, the NFU is urging the Department for Transport to raise the Renewable Transport Fuel Obligation, to play a part in addressing adverse market conditions.
Find out about the legislation changes here.
The biofuel industry represents a valuable outlet for UK wheat, which is currently in surplus, and is a supplier of high protein animal feed, for which the UK is in deficit.
The NFU’s farmer expert on biofuels and crops board chairman for the North East, Brett Askew, said: “The biofuel industry has led the way in demonstrating standards on-farm in the UK, across Europe and in subsequently raising sustainability around the world.
“With legislation limiting the amount of crops used for biofuel to address concerns about Indirect Land Use Change, and bringing certainty to the status of the Renewable Energy Directive, it is time for our government to put the RTFO back on track towards meeting the UK’s 10 per cent biofuel commitment."
Grant Pearson, Commercial Director of Ensus UK, said: “We would urge the UK and other European governments to implement the amended RED as quickly as possible as it will open up the possibility for E10 product to be rolled out across Europe, providing a basis for improved supply and demand balance. The decarbonisation of the transport sector is one of the UK government’s key commitments under the Climate Change Act.”