Abstract: A system and method are provided for implementing a secure configuration of a networked system for secure communications, the networked system including at least one instrument for performing corresponding tasks and at least one controller for controlling functions of the at least one instrument. The method includes providing a secure instrument configuration (SIC); displaying status provided by the SIC server identifying the controller and the instruments to a user via a user interface; writing controller secure configuration information from the SIC server to the controller through a software agent on the controller, the controller secure configuration information including authentication data for the instruments, and/or credentials of the one controller acceptable by the one instruments for identifying the controller; and communicating with the controller to initiate implementation of the secure configuration.