The potential of microrobots to bring about revolutionary changes over micro-operation demands is increasing day to day. This paper presents a controller to provide 5 degrees of freedom for an underactuated bio-inspired helical swimming microrobot. The considered system is a helical swimming microrobot with three flagella in a low Reynolds performance environment. Control of the considered system is performed to reach any desired location, roll angle and pitch angle. The proposed controlling error definition extracted from the system geometry is general for similar actuation configurations. An error detection method for multi-propulsion-unit systems is utilized for 5-DOF micromanipulation of an underactuated bio-inspired helical swimming microrobot by fuzzy-PI controller. A fuzzy-PI controller is proposed to use modified experimental data of PI controller debugging to maintain a suitable efficient control. The comparison of two other possible controllers and the proposed fuzzy-PI controller is discussed, and the performance of trajectory tracking is evaluated by simulations.