This paper presents a method to improve the robustness of the position control of a small permanent magnet within a living organism, such as the human body in microsurgery. So far, position control has been achieved up to 5 Degrees of Freedom with robustness against predicted and modelled disturbance. In order to achieve robust control against non predicted disturbances, the use of a disturbance observer was proved efficient in the past. Disturbance observers require fast and accurate position sensing, which has been achieved so far by optical position sensing. In an effort to extend the operational range of magnetic levitation systems, this paper also considers the use of a position sensor which does not rely on optical sensors, but inductance variation. The models for simulations are based on the Octomag system, which is one of the most up-To-date magnetic levitation devices.