An infectious waste treatment system and method for decontaminating infectious waste employ a thermal friction extruder (20) in which first and second interleaved counter-rotatable augers (40, 42) driven by a variable speed motor include reverse pitch flight sections (62, 72) that urge waste material in a direction opposite to that of the flow stream and into engagement with the back sides of friction plates (50, 52). This increases the amount of heat generated by the extruder. The reverse pitch flight sections can be selectively replaced with forward pitch flight sections to control the amount of heat imparted to the waste material by the friction plates. The size of gaps between the friction plates and the augers is selected along with the motor speed to impart enough heat and friction to the waste material, such that the resulting processed material has an increased BTU value, a consistency and aggregate size such that it can readily be injected as fuel into a cement kilns fuel injection system, thereby completely disposing of the material.
