The problems associated with the greenhouse effect have increased the desire to limit carbon dioxide (CO2) emissions into the atmosphere, including emissions produced by shipboard electrical power systems. This has led to a further search for solutions in this area, such as shipboard hybrid electric power systems (SHEPSs). These systems do not yet have a wide application compared with traditional shipboard electrical power systems for several reasons, including the lack of studies establishing the fault tolerance of such systems. Therefore, in this work, problems related to generated power quality deterioration under large disturbances are studied. To achieve the fault-free operation of SHEPS, an emergency prevention control (EPC) system based on controlled parameter forecasting, along with a system structure and operation algorithm, is developed. The goals of improving electrical power quality are achieved by increasing the control efficiency of the power system’s generating sources. To validate the feasibility of the proposed control system, a computer simulation was carried out after developing a mathematical model of the SHEPS under study. The results of the study show that the use of the proposed EPC system will improve power quality when the controlled parameters are within acceptable limits. At the same time, further research is needed, as the problem of false control action as a consequence of EPC system hardware or software faults remains unstudied.