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This paper focuses on handling disturbances and uncertainty management in Manufacturing Execution Systems (MES). The conception of behaviour-based shop-floor control is discussed. An attempt will be made to demonstrate the usability of behaviour-based control (BBC) in the field of MES. The general state of the manufacturing process is categorized into four classes. According to the classification the appropriate action could be selected. The paper also deals Cockpit Task Management (CTM). Coupled with BBC they offer promising solution for disturbances handling in MES's. A multi-objective rescheduling approach for supporting uncertainty management is also discussed.