A method for operating a vacuum processing apparatus, the vacuum processing apparatus including: a plurality of cassette stands on which a cassette capable of housing a plurality of wafers therein can be placed; a plurality of vacuum processing vessels each having a processing chamber arranged therein, wherein the wafer is arranged and processed in the processing chamber; and at least one transport robot transporting the wafer on a transport path between either one of the plurality of cassettes and the plurality of vacuum processing vessels, the vacuum processing apparatus sequentially transporting in a predetermined transport order the plurality of wafers from either one of the plurality of cassettes to a predetermined one of the plurality of vacuum processing vessels and processing the plurality of wafers. The method includes a number determining step, a remaining-time determining step and a transport order skip step.