The Michelin-starred chef has confirmed he will no longer front the show after mentoring aspiring professional chefs on the programme for six years.
It is understood that Roux had been unable to come to a deal about the level of his commercial activity, which included a deal with potato firm Albert Bartless, for which he was an ambassador.
He said today that negotiating with the BBC was a "frustrating process" and criticised the corporation for failing to grasp "the realities of today's commercial world".
Roux, 53, said: “This hasn't been an easy decision for me to make. I love working with the BBC, and am very proud of how we have built up the popularity and success of these two iconic shows.
“It's not for lack of trying, but sometimes negotiating with the BBC can be a frustrating process, and there are times when I have wondered if the corporation understands the realities of today's commercial world.
Sad day for all concerned but I am and always will be the master of my own destiny.— Michel Roux Jr (@michelrouxjr) March 11, 2014
“The BBC needs to recognise the value of the talent they work with, and also that, whilst we love to be associated with top-quality television, we have other professional commitments that are as important to us as programme-making.”
A spokeswoman for MasterChef said: “MasterChef is sad to announce, after a very happy relationship with Michel Roux Jr as one of the judges on the Professional series, that he will no longer be appearing on the BBC due to a conflict in commercial interests.
“Chef Michel has been a committed and extremely well-loved and respected member of the MasterChef team, an inspiration for the young chefs who have appeared on the show and those he works with on behalf of MasterChef off camera. We wish him the very best of luck in everything he does.”
The BBC said: “Sadly we can confirm that Michel Roux has decided to leave MasterChef The Professionals and Food And Drink due to a conflict in his commercial interests.
“It has been a great privilege to work with such an accomplished professional in his field and we would like to thank him for the huge contribution he has made to those programmes. We would like to wish him well and the best for the future.”
Roux, the son of Michelin-starred Albert Roux, began working as a chef almost 38 years ago and has long been renowned for his Le Gavroche restaurant in London's Mayfair.
He has said he will honour his commitment to presenting a new BBC4 documentary, Chocolat, which begins filming in the next few weeks.
With additional reporting from the Press AssociationReuse content