The article studies the factors influencing the quality of electricity in the power supply systems of sea vessels. Problems caused by electromagnetic interference on ships including voltage drop in the electrical networks due to the nonlinear loads in the system, as well as power asymmetry are considered. The necessity of using active filters in autonomous power systems is found out. A model of an active filter for a closed power supply system with a nonlinear asymmetric load has been developed. The diagram of the active filter model in MATLAB / Simulink environment is illustrated. The simulation was carried out paying attention to various parameters of the system. There has been given an example of a program code for transforming the abc coordinates to the dq coordinates. The disadvantage of the considered circuit is stated: the greater the asymmetry and nonlinearity of the load, the lower the power for current filtering. There are considered the dependences between the measured value of voltage harmonic distortion (according to International Electronic Commission (IEC) 61000-2-4: 2002) and the observed phenomena in the unit; the measured value of the harmonic current distortion and the observed phenomena in the unit. According to the simulation results, it was inferred that the active current compensating filter will improve the quality of power on board the ship. The filter eliminates the imbalance, evens current harmonics and compensates the reactive component of currents. The scheme is advisable for using in autonomous systems of limited power on the merchant ships.