Shunt Active Power Filters (SAPF) are proposed for Power Quality (PQ) improvement in perturbed power distribution networks. Conventionally, the 2-level Voltage Source Inverter (VSI) topology is used in three-phase four wire power distribution networks to mitigate current harmonics and to enhance Power Factor (PF). The Multilevel Inverter (MI) such as the Flying-Capacitor (FLC) topology is competitive with the conventionally inverters for the same targets on low voltage domain, in addition to its performance in medium voltage. In this work a comparative study of two SAPF topologies is proposed. We compare the performance for the two structures for the same modulation, same current and voltage regulation method, same control strategy using modified formulation of the p-q strategy. Firstly, it is demonstrated that the neutral current can be reduced in the conventionally 2-level structure by using a Phase Shift PWM (PSPWM) modulation instead of Sinusoidal PWM (SPWM) modulation. Secondly, peaks of source currents are reduced in the transient state by action on the Pass Band of the DC voltage regulator. Thirdly, comparison between the sizes of the inductance of the filters is made, voltage stresses on the electronic components are compared and harmonic generated by the output voltages of VSI are compared. It is demonstrated the superiority of the FLC over the two-level topology.