A control system of a water heater apparatus with a combustible gas burner is presented where the apparatus includes a pilot burner with an intermittent-type pilot flame, a main burner, a pilot valve and a main valve, a control unit, a flame detection electrode, introduced into the flame of the pilot burner, and which is configured to conduct an ionization current. The control unit is configured to measure/detect a variation involving increase/decrease of the intensity of ionization current detected, the variation in intensity of ionization current being generated during the change between a first condition, in which the ionization current identifies the ignition state of only the pilot burner, and a second condition, in which the ionization current identifies the simultaneous ignition state of the pilot burner and the main burner so that, by detection of the measurement/variation of ionization current, the effective ignition of the main burner is recognized.