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The reconfiguration of control software is regarded as an important ability to enhance the effectiveness and efficiency in future manufacturing systems. Agent technology is considered as a promising approach to provide reconfiguration abilities, but existing work has been focused mainly on the reconfiguration of higher layers concerned with production scheduling and planning. In this paper, we present an automation agent architecture for controlling physical components that integrates “on the fly” reconfiguration abilities on the low-level layer. Our approach is combined with an ontological representation of the low-level functionality at the high-level control layer, which is able to reason and initiate reconfiguration processes to modify the low-level control (LLC). As current control systems are mostly based on standards and principles that do not support reconfiguration, leading to rigid control software architectures, we base our approach on the promising Standard IEC 61499 for the LLC, extended by an innovative reconfiguration infrastructure. We demonstrate this approach with a case study of a reconfiguration process that modifies the LLC functionality provided by the automation agent of a physical component. Thereby, we obtain the ability to support numerous different LLC configurations without increasing the LLC's complexity. By applying our automation agent architecture, we enhance not only the flexibility of each component's control software, but also achieve the precondition for reconfiguring the entire manufacturing system.