Electro-hydraulic shaking tables are widely used for vibration testing where high force and displacement amplitudes are required. In particular, they are a vital tool in seismic testing, enabling the development of buildings and other structures which are earthquake resistant. Three-variable-control (TVC) is commonly used for the control of multi-degrees of freedom (DOFs) electro-hydraulic shaking tables. However, the coupling between the DOFs is often significant and is not compensated by TVC. In this paper, an acceleration decoupling control (ADC) method is presented for a 6 DOFs electro-hydraulic shaking table system to improve the acceleration tracking performance and decouple the motion in task space. The gravitational, Coriolis, and centripetal forces are compensated for in joint space based on a dynamic model of the shaking table. Modal control is used to transform the coupled dynamics into six independent systems. Inverse dynamics models are used to cancel the differences in actuator dynamics. The proportional gains in modal space are tuned heuristically to give sufficient stability margins to provide robustness in the presence of modeling errors. The input filter and feedforward controller in TVC are added to improve the acceleration tracking performance of each independent system. Experimental acceleration frequency responses are used to demonstrate the effectiveness of ADC, and in particular these show a consistent reduction in cross-axis coupling compared to TVC. Moreover, only four parameters need to be tuned, as opposed to 36 for TVC, and the method provides a viable route to improving the accuracy of seismic testing in the future.