An infectious waste treatment system and method for decontaminating infectious waste employ a thermal friction extruder in which first and second interleaved counter-rotatable augers include reverse pitch flight sections that urge waste material in a direction opposite to that of the flow stream and into engagement with the back sides of friction plates. 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.