An apparatus for removal of waste material in a process for extracting puree, or juice, from a starting product based on vegetable or animal food including a step of feeding a measured amount of starting product to a machine for extracting puree. The starting product can be pre-treated, for example softened, and then subject to an extraction step, obtaining a main product including the puree, which is discharged via a first outlet, and a waste material that is discharged via a second outlet. The waste material is then mixed with a measured amount of a liquid, for example water, obtaining a heterogeneous mixture. The heterogeneous mixture can be thus easily removed by suction, for example by a hydraulic pump connected to the second outlet, to be quickly withdrawn from the extraction section avoiding the risk of jamming the machine at the second outlet.