The Fairtrade logo will be removed from all Cadbury chocolate packs worldwide by the end of the year, being replaced by "Cocoa Life" - a brand owned by Cadbury's parent, company Mondelez.
Cadbury insists it will continue to work with Fairtrade and implement much of the original initiative in its programme, but it has come under fire from Fairtrade Australia and New Zealand boss Molly Harriss Olson.
Ms Olson told news.com.au she wished Cadbury had stuck with Fairtrade, saying their relationship with the world's second-largest chocolate manufacturer will change.
"It will be a new partnership, a different sort of partnership," she said.
The move by Cadbury conflicts with other chocolate brands Nestle and Ferrero, which have expanded the Fairtrade mark across their respective businesses.
Fairtrade says it helps more than 1.5 million farmers in 75 countries around the world, making sure they get a fair price for their product.
Cadbury said Fairtrade will continue to be "independently involved" in the Cocoa Life program "to give consumers the confidence that... they are helping cocoa-farming communities to thrive."
Ms Olson said she's optimistic for the future of the two brands, hoping that working together will provide better coverage for all products.
"We want to help them, to monitor the new phase of the program which will have a much wider reach," she said.
Despite the change, Ms Olsen said Fairtrade will still monitor Cadbury and other brands under Mondelez.
"The Fairtrade logo is the most trusted model of certification and no corporate label will ever have that independent level of respect that Fairtrade has," she said.
"If at any point, any company we're working with starts to think they can grade their own homework and hide behind a fair washing plan to confuse the public, we will call it out and alert consumers."