A slave manipulator manipulates a medical device in response to operator manipulation of an input device through joint control systems. The stiffness and strength of the slave manipulator are adjustable according to criteria such as the mode of operation of the slave manipulator, the functional type of the medical device currently being held by the slave manipulator, and the current phase of a medical procedure being performed using the slave manipulator by changing corresponding parameters of the control system. For safety purposes, such changes are not made until it is determined that it can be done in a smooth manner without causing jerking of the medical device. Further, an excessive force warning may be provided to surgery staff when excessive forces are being commanded on the slave manipulator for more than a specified period of time.