A system and method of variable velocity control of an instrument by a computer-assisted device includes a computer-assisted device that includes an actuator and one or more processors. To perform an operation with an instrument coupled to the computer-assisted device, the one or more processors are configured to set a velocity set point of the actuator to an initial velocity, monitor force or torque applied by the actuator to actuate the instrument, when the applied force or torque is above a first force or torque limit, determine whether a total duration of a set of pauses occurring during the operation of the instrument is below a maximum pause threshold, and in response to determining that the total duration is below the maximum pause threshold, pause the operation of the instrument.