Integration of factory level advanced process control (FL-APC) system and tool level advanced process control (TL-APC) system using selectable APC operation modes indicating different operational settings for the FL-APC system and at least one TL-APC system is disclosed. During operation, the FL-APC system controls operation of the TL-APC system. The invention allows a manufacturing execution system (MES) to have additional capability to run the process control functions at FL-APC system and/or TL-APC system, and allows integration of a variety of different tools with a TL-APC system. An implementation method, system and program product are also disclosed.