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In a complex manufacturing environment the ability to handle unexpected events is from crucial importance. Due to their distributed nature, multi-agent system provides a convenient way to enable failure tolerance. This paper presents a multi-agent architecture where the agents are combined with an ontology and subjacent low-level based on IEC61499 standard in order to enhance fault tolerance in such complex systems. We propose a hybrid approach for fault tolerance, where different types of agents are using different heartbeat mechanisms to detect exceptional events. The comparison with other related approaches shows its applicability with a reduced message flow at the same time.