The plant was discovered in a raid in Crossmagalen, County Armagh on Tuesday.
A man arrested in connection with the find has been released on bail pending further enquiries.
HMRC officers, accompanied by the Police Service of Northern Ireland (PSNI), seized six storage tanks, 37,000 litres of illicit fuel, 1,000 litres of acid, pumps and associated equipment.
Almost 21,000 litres of toxic waste, stored in barrels and in an underground slurry pit, were also removed from the site.
Clare Merrills from Revenue and Customs said the plant was three times larger than any other plant found in the UK.
And from the breakingnews.ie report
HMRC assistant director of criminal investigation John Whiting said: “This is fuel fraud on an industrial scale.
“The sheer size of this illegal operation is staggering and far exceeds anything we have ever come across before.
“This activity would have generated massive revenue loss as well as tonnes of toxic waste – it’s economic and environmental impact on Northern Ireland would have been considerable.”
He added: “The location of this illegal operation would suggest that the fuel was destined for both sides of the border, resulting in losses to both the UK and Republic of Ireland exchequers.
“This operation shows the success of multi-agency co-operation in tackling fuel fraud and why we will continue to work with our partners, as part of the Organised Crime Task Force, in the fight against organised crime.”