The substrate processing apparatus relating to the present invention comprises a polishing section where wafers are sequentially arranged, and that has multiple polishing platens for polishing a metal film on the wafer surface in stages. The wafers are simultaneously conveyed between the polishing platens by a rotating head mechanism. Further, the wafers polished by the polishing platen for the final stage polishing are sequentially conveyed to a cleaning section and are cleaned. The wafers from the polishing section to the cleaning section are conveyed by a load-unload unit, a post-polishing wafer reversal unit and wet robots. Then, the operation of each part is controlled by an apparatus controller to start the cleaning processing of the polished wafers by the polishing platen for the final stage polishing within a predetermined time period from the completion of polishing by the polishing platen for the final stage polishing. With this control, corrosion to wiring containing corrodible metal, such as copper, can be assuredly prevented.