The present invention discloses a method and a device for controlling the operation of a dual fuel engine. In the dual fuel engine using an FCT technology, a new FCT configuration of an FCT shaft (42) is used to allow transitioning between a liquid fuel mode and a gaseous fuel mode at higher engine loads. According to the new configuration, a liquid fuel main injection is performed relatively late when switching from the liquid fuel mode to the gaseous fuel mode, and in a liquid fuel part load mode. A pilot injection system (60) of the engine is used to provide an early liquid fuel pilot injection during the transition and also in a liquid fuel part load mode to facilitate operating the engine in said mode with the late main injection timing.