This paper proposes a model based trajectory tracking control scheme for under-actuated underwater robotic vehicles. The difficulty in stabilizing a non-linear system using smooth static state feedback law means that the design of a feedback controller for an under-actuated system is somewhat challenging. A necessary condition for the asymptotic stability of an under-actuated vehicle about a single equilibrium is that its gravitational field has nonzero elements corresponding to non-actuated dynamics. To overcome this condition, we propose a continuous time-varying control law based on the direct estimation of vehicle dynamic variables such as inertia, damping and Coriolis & centripetal terms. This can work satisfactorily under commonly encountered uncertainties such as an ocean current and parameter variations. The proposed control law cancels the non-linearities in the vehicle dynamics by introducing non-linear elements in the input side. Knowledge of the bounds on uncertain terms is not required and it is conceptually simple and easy to implement. The controller parameter values are designed using the Taguchi robust design approach and the control law is verified analytically to be robust under uncertainties, including external disturbances and current. A comparison of the controller performance with that of a linear proportional-integral-derivative (PID) controller and sliding mode controller are also provided.