In the controller of a machining center in accordance with the present invention, a plurality of heads or cutters are connected to control shafts of a plurality of control systems, respectively, and are controlled independently by individual programs. The controller includes instruction means for giving a stand-by instruction or stand-by release instruction to the control systems in synchronism with one another and timing setting means for setting a timing of a stand-by instruction or a stand-by release instruction for which synchronization is established between the systems by the instruction means so that a timing of stand-by or stand-by release set for the program of one particular system determines a timing of stand-by control by the program of another particular system. Accordingly, a stand-by system and a system to be released from a stand-by state can be designated arbitrarily and control of a machine tool can be made efficiently.