In an internal combustion engine equipped with a pair of intake ports for each cylinder and capable of controlling a quantity of air entering the engine by controlling an intake valve open timing and an intake valve closure timing of each of a pair of intake valves located in the respective intake ports, a two-intake-valve operating mode is used in a high-load, high-speed operating range, whereas a one-intake-valve operating mode is used in predetermined low- and mid-load, low- and mid-speed operating ranges to create a great gas flow within the cylinder. A fuel injector is located in a first one of the intake ports to allow air flow through the first intake port over all operating ranges. An electronic engine control unit switches a compensating mode for an injection amount of fuel injected by the injector, based on changes in a quantity of wall fuel mass flow adhered onto the inner wall surface of the intake port during transient operating conditions, from one of a first compensating mode which is preprogrammed to be suitable for the one-intake-valve operating mode and a second compensating mode which is preprogrammed to be suitable for the two-intake-valve operating mode to the other.