It follows accusations of indecent behaviour, including flashing at the cast on Doctor Who and its spin-off Torchwood.
An ITV spokesperson confirmed: "We thank John for two brilliant years on the Dancing on Ice panel and are pleased to be working with him again as host of the forthcoming All Star Musicals specials."
A source told The Sun: "This will be devastating for him. Clearly ITV feel it’s not a good look to have someone like John centre-stage on a family-friendly show."
Dancing On Ice returns in January on ITV. Casting announcements are to be revealed in due course.