An engine ECU executes a program including the steps of: detecting an engine speed NE, a throttle angle THA and an amount of intake air GA; estimating an amount of intake air GAINI from the engine speed NE and the throttle angle THA; if the estimated amount of intake air GAINI minus the detected amount of intake air GA is larger than a predetermined deviation .DELTA.GA(0) (YES at S104), then causing an intake manifold injector to inject fuel to clear a deposit, as controlled, at the exhaust stroke when an intake valve is closed and at the intake stroke when the intake valve is opened and an exhaust valve is closed.