Techniques for detecting errors or loss of accuracy in a surgical robotic system

Systems and methods for operating a robotic surgical system are provided. The system includes a surgical tool, a manipulator comprising a base supporting links for controlling the tool, a navigation system comprising a tracker coupled to the tool and a localizer to monitor a state of the tracker. A controller acquires raw kinematic measurement data about a state of the tool relative to the base from the manipulator, known relationship data about the state of the tracker relative to the tool, and raw navigation data about the state of the tracker relative to the localizer from the navigation system. The controller combines this data to determine a raw relationship between the base and the localizer. The raw relationship is filtered for controlling the manipulator. The raw relationship or a less filtered version of the raw relationship is utilized to determine whether an error has occurred in the system.