Hayes is thought to have left the Bolton-based bread maker within the past few weeks.
It is not known why he left, nor if he is to be replaced. Hayes joined Warburtons in the summer of 2007.
In April last year, Warburtons appointed former Durex marketer Megan Harrison to its number-two marketing role.
Hayes joined Warburtons from the distiller Whyte & Mackay, where he was marketing director and was responsible for the relaunch of the eponymous whisky brand.
Warburton's bakery products range includes Warburtons 800g Toastie, the 800g Soft Farmhouse and 800g Wholemeal. It has also launched a range of gluten-free and wheat-free bakery products.
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