Challenges for using robots in operational centrifuges are robust structures with low mass, mechanical design for movement at high vibration and high gravity (gs), orientation of components to avoid deflection, and advanced controllers to reduce vibration. The importance of centrifuge modelling resides in the capacity of physical simulation of large scale models with a small scale model. This paper presents the novel design and development of a flexible actuation control system (FACS) to control multiple stepper motors that use robots within an operational centrifuge. The novel design is robust and symmetric in order to withstand forces equivalent to 30 times earth’s gravitational acceleration (30g). Moreover, the FACS and its control software are flexible and generic in order to serve for different applications. The components of the system were selected and the components’ layout (location and orientation) was designed to support 30gs and fit within a box of 42 cm × 34 cm × 22 cm. A graphical user interface was developed in LabVIEW to control four motors. Different types of motion control such as judge, jog, synchronized, unsynchronized, absolute and relative positioning were implemented. The FACS was validated with a cone penetration test (CPT) and the results are discussed. An actuator was used to perform the CPT whilst the centrifuge was rotating and achieving 30gs. The case study probed the flexible application of the FACS, its robustness to g field and its performance.