A medical robotic system includes a surgical instrument, a robotic arm assembly, an input device, and a processor. The surgical instrument has an end effector and a sensor for sensing a force exerted by the end effector, and is operatively mounted on the robotic arm assembly. The processor is configured to receive commanded movement of the end effector from the input device, receive information of the force from the sensor, determine a reduced velocity of the commanded movement that would inhibit damage causing motion of the end effector, and control robotic manipulation of the surgical instrument in response to the commanded movement of the end effector while restricting the velocity of the commanded movement to the reduced velocity.
