In a vacuum processing apparatus having a plurality of vacuum processing chambers at least one of which are coupled to each of a plurality of vacuum transfer chambers which are behind an atmospheric transfer chamber and have vacuum transfer robots in their interior to transfer a wafer, taking out a plurality of wafers in a cassette and transferring successively to the plurality of the vacuum processing chambers, and thereafter returning to the cassette, the wafers are controlled to be transferred to all of the vacuum processing chambers coupled to the backmost vacuum transfer chamber and thereafter a next wafer is transferred to a vacuum processing chamber which becomes possible for the next wafer to be transferred in before they are possible to be transferred out from the vacuum processing chambers coupled to the backmost vacuum transfer chamber and arranged backmost.