The aim of the paper is to propose a navigation strategy applied to a class of rotorcraft having a free rodsuspended load. The presented approach relies on the Linear Kalman Filter to estimate the not only the state vector but also a generalized disturbance term containing parametric, couplings and external uncertainties. A simple hierarchical control is used to drive the motion of the rotorcraft, which is thus updated with the estimation of the disturbance evolving during the a navigation task. Despite the time-scale separation due to the underactuated nature of the flying robot, the estimation approach has shown its effectiveness considering the same sampling time. A detailed simulation model is used to evaluate the performance of the proposal under different disturbed scenarios.