Abstract: A diesel engine, having a plurality of individually controllable fuel injected cylinders, is operated in a skip firing mode to reduce smoke emissions during low power operation. The system senses certain identified engine operating parameters and when these parameters exceed predetermined thresholds for a predetermined time, then the skip firing is implemented. In another embodiment, it is possible to implement several different skip firing patterns dependent upon engine performance. Upon implementation of skip firing, the engine timing angle is reset by a fixed angle and a multiplication factor is included in the speed loop integrator to ensure that the appropriate fuel volume value is injected into each cylinder immediately upon initiation of skip firing. Skip firing is then disabled when another set of predetermined conditions is satisfied.