A security system for controlling access to motion control systems. The security system limits access to application programming interface (API) functions. The limitations on API functions can be implemented as a denial of access to certain restricted functions and/or as a limitation on certain controlled parameters employed by certain restricted functions. The security system may allow or disallow access based on users or accounts. The security system may also be programmed to prevent access to certain functions arbitrarily as determined by a system administrator or on criteria such as the status of the system.