The manuscript presents a new method of tooth cutting for worm, spiroid and bevel gearwheels by means of running-in cutter heads and results of its practical application. An example of upgrading the milling machining center is considered; the schemes prior to and after its upgrade are shown. The technique for calculating the control program parameters of gearwheel tooth cutting is described. The manuscript shows examples of controlling the contact pattern location for spiroid gears by introducing the machine-tool setting parameter correction to eliminate the negative effect of cutting forces. The schemes of tooth cutting by a hob and by a running-in cutter head are shown with indication of components for cutting forces arising at hobbing. Possible layout versions of the running-in cutter head design with replaceable carbide inserts are considered. Advantages of the system approach to controlling the preparation of a manufacturing operation are highlighted. The manuscript describes the parts of a system for preparation of automated manufacturing operations of tooth cutting by means of running-in cutter heads such as specification, data, constraints and methods and their interrelations. Examples of practical implementation of the described method of tooth cutting for single and series production of spiroid gears are given, and its advantages are discussed.