In this paper, a nonlinear controller for tracking a desired trajectory for an underactuated hovercraft is considered. It is a modification of a method known from the literature. However, the control algorithm considered here has two important features that differ from the mentioned control strategy. First, it concerns the case when the center of mass does not coincide with the geometric center, which results in additional forces and moments of force. The lack of symmetry causes the original trajectory tracking method not to take this fact into account, while the proposed approach is a generalization of the known concept. Here, a diagonalization of the inertia matrix has been applied, by means of a velocity transformation, which made it possible to reduce the symmetric matrix to a diagonal form. Secondly, the transformed quasi-velocity equations of motion allow some insight into the dynamics of the vehicle as it moves, which was not shown in the source work. The offered approach was verified by numerical tests for a hovercraft model with three DOF and for two desired trajectories. The method can be useful in preliminary simulation studies at the controller selection stage without experimental validation.