A control apparatus is disclosed which controls both a fuel injection system and an exhaust gas cleaning system for an internal combustion engine. The fuel injection system includes at least one fuel injector for injecting fuel from a fuel source into a cylinder of the engine. The exhaust gas cleaning system includes a fuel adding device for adding fuel from the fuel source to the exhaust gas from the engine. The control apparatus includes determining means and stopping means. The determining means determines whether operation of the fuel adding device for adding the fuel to the exhaust gas interferes with control by the control apparatus of the fuel injection system. The stopping means stops the operation of the fuel adding device when it is determined by the determining means that the operation of the fuel adding device interferes with the control by the control apparatus of the fuel injection system.