The chef and presenter blasted the "frustrating process" of trying to negotiate with the Beeb and said he questioned if the BBC understood "the realities of today's commercial world".
It is understood that Roux - who has become well-known to viewers for fronting 'MasterChef: The Professionals' for six years and reviving the series 'Food And Drink' - had been unable to come to a deal about the level of his commercial activity.
Among his advertising commitments has been a deal with potato firm Albert Bartlett, for which he was an ambassador.
Roux, 53, who has two Michelin stars, said today: "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.
"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."
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.
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."
Roux has said he will honour his commitment to presenting a new BBC4 documentary, 'Chocolat', which begins filming in the next few weeks.