Several thousand cannabis plants with an estimated street value of £1m were seized in a raid on RGHQ Chilmark.
Five men and a teenager were arrested on suspicion of cannabis production after the midnight raid on Wednesday.
There are 20 rooms in the building with almost every one converted for the wholesale production of cannabis plants, police said.
The former Ministry of Defence bunker was built in the 1980s to protect local dignitaries and government officials in the event of a nuclear attack.
Described as "almost completely impenetrable", Wiltshire Police had to wait for the suspects to leave the bunker before they could gain access.
Det Insp Paul Franklin, said it was only after getting through the nuclear blast doors, that the "enormous set up" was discovered.
"There are approximately 20 rooms in the building, split over two floors, each 200ft long and 70ft wide," he said.
"Almost every single room had been converted for the wholesale production of cannabis plants, and there was a large amount of evidence of previous crops."
He added that he was convinced it was "one of the largest crops ever discovered" in the county.
A teenager and two men, aged 15, 19, and 37, all of no fixed abode, were arrested on suspicion of cannabis production.
A further three men, aged 27, 30 and 45, all from Somerset, were arrested on suspicion of cannabis production and human trafficking offences.
A large-scale cannabis factory has been found in an underground former nuclear bunker, Wiltshire police have said.