A mask portion is provided at a partial area of an intake port at a side opposite to an exhaust port. The mask portion prevents a part of the intake port from being opened when the intake valve is in a low lift state. A top surface of a piston includes a smooth surface. An ECU sets the maximum lift of the intake valve for a variable valve mechanism to an intermediate lift and sets a fuel injection timing for an injector to a compression stroke when an operating range of the engine is a fast idle range. The intermediate lift is an amount of lift at which the intake valve is moved beyond the mask portion and a flow rate of intake air in the partial area is limited relative to a flow rate of the intake air in other areas owing to the mask portion.