An electronic control system has an engine control computer and a throttle control computer. The engine control computer has a monitor program separate from an engine control program. The monitor program is for checking the operation of the throttle control computer and executed by the engine control computer as a timer interrupt routine. A watch dog timer is connected to the engine control computer to detect malfunction of the monitor program in response to a watch dog pulse produced during the execution of the monitor program. The watch dog timer disables an electronic throttle control by the throttle control computer upon detection of the malfunction of the monitor program. At the same time, the engine control mode is changed from a normal engine control to an engine power reduction control thereby to ensure a limp-home operation of the engine.