Bakker, who was part of the launch team that brought the music channel to Europe, does not have a new job.
MTV said his responsibilities would be split between Heather Jones, senior vice-president and managing director of music and comedy, and Richard Tan, senior vice-president of finance and operations until a successor is appointed.
As well as establishing MTV Network's ad sales arm Viacom Brand Solutions in 2000, Bakker launched video broadband channels MTV Overdrive and MTV Flux.
He was also responsible for children's channel Nickelodeon UK and Paramount Comedy.
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