The controller for a machine tool according to the present invention makes it possible to discharge both a coolant and an oil mist from a through hole provided in the tool equipped to a main axis of a machine tool, allows a processing program to instruct the discharge of either the coolant or the oil mist, and carries out such a control that a state where the above-described tool is detached from the main axis is maintained during a predetermined period of time at the time of replacing the tool, and at the same time, the oil mist is discharged from the above-described oil mist unit so as to remove the coolant from the above-described piping during the predetermined period of time.