John Watson Snr, 49, and Mindaugus Aleksandravicius, 49, led a 12-man gang that flooded northern England with fake cigarettes worth £10million.
They were found guilty of excise fraud and jailed at Sheffield Crown Court last year after being busted by HM Revenue and Customs (HMRC) in 2015.
Officials said the factory - which could produce 140 packets of cigarettes a minute - was the largest they had "ever come across".
Now they have been hauled back before the same court where a judge ruled Watson Snr, of Doncaster, must pay back £412,000 or face a longer stretch inside.
At the same confiscation hearing, held on anuary 4 and 5, Aleksandravicius was ordered to repay £2,760 within three months.
Confiscation proceedings against other members of the gang are ongoing.
Gillian Hilton, assistant director at the HMRC's fraud investigation service, said: “Watson and his associates ran highly sophisticated illegal operation, which put millions of counterfeit cigarettes on the streets of the UK and deprived our vital public services of millions of pounds.
“Now Watson must pay back his ill-gotten gains or spend more time behind bars and still owe the money.
“Our work doesn’t stop when someone is convicted – HMRC always looks to recover proceeds from crime from criminals who try to cheat the system."
HMRC carried out coordinated raids at properties linked to the gang in County Durham and South Yorkshire in November 2015.
Officers discovered the largest tobacco factory ever encountered by HMRC inside a farm unit in Crook, County Durham.
The factory had more than 24 tonnes of tobacco inside, along with 500,000 cigarettes, old tobacco machinery and products used to make the cigarettes.
Officers also discovered caravans that were being used by the factory workforce.
The cigarettes produced at the factory were moved to a nearby garden centre, before being distributed to locations in the North East and South Yorkshire.
Watson Snr said he earned less than £15,000 a year at the time, but investigators discovered he'd splashed out more than £180,000 on luxury cars and a holiday.
Seven of the men admitted excise fraud at separate hearings at Leeds and Sheffield Crown Court in 2019.
The remaining five men were found guilty of excise fraud in February 2020 following a trial at Sheffield Crown Court.
In total, HMRC seized cigarettes, tobacco and associated paraphernalia capable of evading more than £10 million in duty.
Watson and a right-hand man were responsible for setting up and running the tobacco factory.
Aleksandravicius oversaw the day-to-day running of the factory, recruited factory workers and arranged movement of cigarettes to a unit at a garden centre.