A controller that controls a machine tool, a method of controlling a machine tool, and a computer program that causes a computer to operate as a controller that controls a machine tool, the machine tool comprising multiple control axes and used for machining by cutting of a work as a machining target by means of coordinated motion of the control axes. The method includes acquiring a position command for driving a cutting tool or the work, acquiring a rotation speed of the rotated cutting tool or the rotated work, calculating oscillation amplitude, calculating an oscillation frequency, calculating an oscillation command for causing the cutting tool and the work to oscillate relative to each other, storing a command route, correcting the oscillation command based on the stored command route, determining a drive signal to be used for driving the servo motor, and outputting the drive signal.