In a control apparatus for a wind turbine generator system, a wind turbine classifying unit classifies a plurality of wind turbines into a first wind turbine group that does not satisfy a rated wind speed condition and a second wind turbine group that satisfies the rated wind speed condition. A first controlling unit releases, for the wind turbines of the first wind turbine group, the output power reducing operation and causes the wind turbines of the first wind turbine group to perform an output power corresponding to a wind condition. A second controlling unit supplements a first deviation, which is a difference between a total output power of the first wind turbine group and a target output power, with an output power from the wind turbine of the second wind turbine group.