Abstract: A rotary sterilization system, a controller for use in the rotary sterilization system, and a method performed by the controller are disclosed. The system, controller, and method are used to administer a sterilization process performed on a line of containers and provide on-line handling of a deviation in a scheduled parameter during the process. The containers contain a shelf stable food product that is to be sterilized in the sterilization process. In addition to the controller, the rotary sterilization system includes a rotary sterilizer. The controller controls the rotary sterilizer in performing the sterilization process according to scheduled parameters. When a deviation in a specific one of the scheduled parameters occurs, the controller identifies those of the containers that will in response have a total lethality predicted to be delivered to them during the sterilization process that is less than a predefined target lethality.