Officers found an estimated 2,000 plants together with £30,000 of growing equipment spread across four large rooms at the building in Engine Lane, Horbury.
It is estimated the value of the plants seized could be around £1million, with the potential for the factory to have produced much more.
The raid follows the discovery of a major cannabis factory on Millennia Park Industrial Estate in Thornes on June 8. In April another large operation was found in a disused building on Kirkgate.
Both of those are thought to have contained plants worth a potential £1million-plus.
Inspector Ian Williams of the Wakefield neighbourhood policing team, said: “This is the third significant seizure of cannabis plants in Wakefield in just over a month and should serve as notice that we will not hesitate to act on intelligence about these sort of operations.
“This latest, and large scale, raid was executed within less than 24 hours of community intelligence reaching us about suspicious activity at the unit and featured a large amount of police resources.
“What we uncovered was clearly a large scale cannabis factory in which all of the large rooms had been kitted out with ventilation equipment suggesting we struck before it was being used to its full production potential.
“Even so, we believe the four rooms we found which were in use contained around 2,000 plants, the yield from which is potentially worth over £1million.”
Neighbourhood officers, detectives, specialist support officers and resources such as police dog units and supported by the police helicopter carried out the raid on Wednesday afternoon after receiving intelligence about suspicious activity there the day before.
Insp Williams added: “I want to thank those residents who are coming forwards with information about cannabis grows in Wakefield and encourage them to keep doing so.
“We have wide ranging enquiries with partners ongoing into all three cannabis factories discovered recently and can promise this is an issue we are taking very seriously indeed.
“Anyone who has information about cannabis production in the city can contact the Wakefield District NPT on 101 or Crimestoppers anonymously on 0800 555 111.”
*Three men aged 45, 38 and 40 of no fixed address have been arrested in connection with the enquiry and remain in custody.