It is shown that the alternate passivity-based control schemes can be designed which explicitly exploit the passivity properties of the Timoshenko model. This approach has the advantage over the conventional methods in the respect that it allows one to deal directly with the system's partial differential equations without resorting to approximations. Numerical results for the tracking control of a translational and rotational flexible Timoshenko arm are presented and compared. They verify that the proposed control schemes are effective at controlling flexible dynamical systems.