About 6,000 litres of laundered fuel was seized when the illegal plant was discovered in remote farm buildings near Clady on Thursday.
The joint police and customs operation also uncovered a lorry which had been adapted to transport fuel, as well as pumping, storage and filtration equipment.
The plant had the capacity to make about 10,000 litres of diesel each week amounting to a weekly revenue loss of up to £5,000, a customs official said.
Cigarettes and tobacco were also uncovered in the Strabane area.
The find came after police and customs officers detected 63 vehicles and seized £30,000 worth of illegal fuel in a day-long operation on Wednesday.
A police spokesman said it was the "biggest ever detection in a one-day operation" involving illegal fuel in the UK.
Filtered
The police said they were determined to track down and prosecute those involved in the black market.
They said it was too early to say who was behind Thursday's discovery but suspect criminal elements rather than paramilitaries at this stage.
A customs spokesman said the discovery of the diesel plant in Clady was "another significant hit on the illegal fuel trade and shows the benefit of close working with the Police Service of Northern Ireland".
"We have repeatedly warned motorists to think before buying cheap fuel," said the spokesperson.
"It puts honest filling stations out of business, robs the taxpayer of money for public services and puts the motorist's vehicle at risk of serious engine damage."
The spokesperson said laundering plants brought additional dangers, as the chemical residue was "often dumped without regard to the local environment".
Inquiries into the fuel laundering operation are continuing.
Agricultural
Last month, a fuel laundering plant with the capacity to make about 50,000 litres of illegal diesel per week was shut down in Moy, also in County Tyrone.
Officials seized 15,000 litres of laundered fuel and 5,000 litres of red diesel.
Laundered fuel is red or green diesel which has been filtered through chemicals or acids to remove the government marker.
The chemicals and acids remain in the fuel and damage fuel pumps in diesel cars.
Red diesel is for use in agricultural machinery, and not for use in road vehicles, in the United Kingdom.
Green diesel is the Republic of Ireland's equivalent.