In a gas turbine engine control system having a first valve for regulating the flow rate of fuel in premixed combustion and a second valve for regulating that in diffusion combustion, when the combustion mode is switched from one mode to the other mode, whichever of the first and second valves is associated with the other combustion mew is opened to supply the amount of fuel required for conducting the other combustion mode and, the opening of the valve associated with the one combustion mode is gradually decreased, while that of the other combustion mode is gradually increased, thereby maintaining the total amount of fuel supplied to the engine constant, after elapse of a predetermined period. At the time of switching the combustion mode, therefore, the total amount of fuel supplied to the engine can be accurately controlled to a desired value to minimize engine speed fluctuation.