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Abstract Anomaly detection in industrial control and cyber-physical systems has gained much attention over the past years due to the increasing modernisation and exposure of industrial environments. Current dangers to the connected industry include the theft of industrial intellectual property, denial of service, or the compromise of cloud components; all of which might result in a cyber-attack across the operational network. However, most scientific work employs device logs, which necessitate substantial understanding and preprocessing before they can be used in anomaly detection. In this paper, we propose a network intrusion detection system (NIDS) architecture based on a deep autoencoder trained on network flow data, which has the advantage of not requiring prior knowledge of the network topology or its underlying architecture. Experimental results show that the proposed model can detect anomalies, caused by distributed denial of service attacks, providing a high detection rate and low false alarms, outperforming the state-of-the-art and a baseline model in an unsupervised learning environment. Furthermore, the deep autoencoder model can detect abnormal behaviour in legitimate devices after an attack. We also demonstrate the suitability of the proposed NIDS in a real industrial plant from the alimentary sector, analysing the false positive rate and the viability of the data generation, filtering and preprocessing procedure for a near real time scenario. The suggested NIDS architecture is a low-cost solution that uses only fifteen network-based features, requires minimal processing, operates in unsupervised mode, and is straightforward to deploy in real-world scenarios.