The indirect energy flow measurement method is extended to cover highly nonlinear, frequency, amplitude and magnetic field dependent magneto-sensitive natural rubber isolators applied in a real vibration isolation system. Energy flow is an effective measure of vibration isolation while being a single quantity that considers both force and velocity. The use of the indirect technique is of interest while requiring only accelerometers since it is usually difficult to directly measure the force in a real application. The vibration isolation system is composed of four magneto-sensitive rubber isolators that are inserted under a vibrating source consisting of a solid aluminium mass excited by an electro-dynamic shaker. Magneto-sensitive rubber isolators are more useful than conventional rubber isolators since the dynamic stiffness varies with the application of an external magnetic field, thus resulting in more effective vibration isolation. Various approximations regarding the indirect technique are investigated, concluding that average stiffness of magneto-sensitive isolators can be used and auto-spectrum of the foundation velocity ignored. In addition, various error analyses are performed. Finally, the indirect measurement of the energy flow is validated by direct measurements, showing very good agreement. (C) 2012 Elsevier Ltd. All rights reserved.