The business said two of the sets will be preserved at the Burton brewery, in a bid to serve as a reminder of its brewing heritage.
The four remaining sets had been used exclusively for fermenting Marston’s Pedigree ale in cask.
However, CMBC said low volumes due to the decline in the UK cask market means the process using the sets was now unviable.
Previously, beer from the sets was blended with beer from stainless-steel fermenters to deliver Marston’s Pedigree in cask but the low volumes had made a move to stainless steel necessary.
The move, which is already used for fermenting Pedigree in bottle and keg, will help ensure a high-quality cask product while delivering improved sustainability and efficiency at the brewery by reducing water and energy consumption, CMBC claimed.
The Union sets, which were also known as the Burton Union System, were first developed in the Victorian era.
According to the Marston’s Brewery website, Pedigree was the only beer to come through the system.
In addition, it is reported Marston’s was the last brewery in England to utilise this system, which used to be used by Bass Brewery.
Director of brewing Emma Gilleland said: “We take great pride in the quality of our brews and by moving cask Pedigree to stainless-steel fermenters, we will be able to deliver consistent, strong quality for our customers and consumers going forwards.
“We are committed to protecting the legacy of the Union sets, both for the brewery and for Burton.
“We will invest in the preserving two Union sets, which will remain at the brewery so they can continue to be part of its future as enduring, iconic symbols of British brewing.”
The Campaign for Real Ale (CAMRA) voiced disappointment at the announcement however, the organisation stated it was reassured CMBC had invested in the site.
Chairman Nik Antona said: "It's obviously hugely disappointing CMBC has taken the decision to retire its iconic Burton Unions. It is arguably the last brewery in the world, and certainly in the UK, using this method to brew beer and this decision will see a unique and historic part of Britain’s brewing heritage declared completely extinct.
“We’d urge CMBC to find some way to preserve these historic pieces of brewing equipment rather than simply scrap them, or make the Union Sets available to another brewery which might be interested in preserving this tradition.
“We do understand the need for breweries to remain efficient and ensure quality at a time when we are sadly seeing many closures. CAMRA is reassured that this news is tempered by the fact CMBC has invested a significant sum, worth several millions, in the site, which hopefully will secure continued brewing and support the cask ales which have long been brewed in Burton-on-Trent.”