Abstract What causes negative loss factors in measuring SEA parameters by the power injection method? Analytical results in this paper show that negative loss factors are caused by non-conservative coupling, and non-conservative coupling does not always increase the effective internal loss factors (EILFs). To study the power flow of non-conservatively coupled systems, some new SEA models for non-conservatively coupled systems were suggested by researchers. However, the SEA parameters for non-conservatively coupled systems have not been extensively discussed by using the model of classical Statistical Energy Analysis (CSEA) up to now. The aim of this study is to give insight into the problem of the energy balance mechanism of non-conservatively coupled systems by using both the model and the energy balance equations in CSEA. A method of calculating EILFs and coupling loss factors (CLFs) for non-conservatively coupled machine structures is introduced. The possibility of causing negative loss factor is investigated by analysis of two non-conservatively coupled oscillators. Furthermore, the influences of the coupling stiffness and the coupling damping on EILFs and CLFs are investigated in detail. Finally, an application example is included to demonstrate the accuracy of the method.