A fully automated analysis procedure and instrument for the measurement of total 99Tc in aged nuclear waste has been developed. The overall analysis approach is based on a fully automated wet radiochemical analysis method. Microwave-assisted sample oxidation is used prior to a chemical separation step in order to oxidize all of the non-pertechnetate species to pertechnetate. Separation of the pertechnetate from interfering radioactive and stable matrix species is carried out using an anion-exchange column. The separated 99Tc is quantified using a flow-through solid cell scintillation detector. The instrument is capable of an analysis time of <13 minute per sample with a detection limit of 2000 dpm/ml. Nuclear waste samples from the Hanford site with a high content of non-pertechnetate species were successfully analyzed using this method.