A system and method of variable velocity control of a surgical instrument in a computer-assisted medical device including an end effector located at a distal end of the instrument, an actuator, and drive mechanisms for coupling force or torque from the actuator to the end effector. To perform an operation with the instrument, the computer-assisted medical device sets a velocity set point of the actuator to an initial velocity, monitors force or torque applied by the actuator, reduces the velocity set point when the applied force or torque is above a first threshold, increases the velocity set point when the applied force or torque is below a second threshold, decreases the velocity set point to zero when the applied force or torque is above a maximum threshold, and drives the actuator based on the velocity set point. The first and second thresholds are lower than the maximum threshold.