A two-gas shaft turbine control system (31) is disclosed. The gas turbine control system comprises a fuel controller (35), which receives a speed error signal, indicating whether the low-pressure turbine wheel (11) of the gas turbine (1) is rotating at the desired target speed. The gas turbine control system (31) further comprises an NGV controller (41), which receives a speed error signal, indicating whether the high-pressure turbine wheel (9) of the gas turbine engine (1) is rotating at the desired target speed. Two cross channel controllers are further provided. On the basis of a gas turbine model, a first cross channel controller (43) provides a fuel control modification signal, which is added to a control signal generated by the fuel controller (35). A second cross channel controller (45) provides an NGV control modification signal. The modification signals are aimed at reducing or canceling the effect of mutual interaction between fuel control and NGV control. A two-shaft gas turbine engine system and a method of operation are further disclosed.