The integration of communication networks and the Internet of Things (IoT) in Industrial Control Systems (ICSs) increases their vulnerability towards cyber-attacks, causing devastating outcomes. Traditional Intrusion Detection Systems (IDSs), which are mainly developed to support Information Technology (IT) systems, count vastly on predefined models and are trained mostly on specific cyber-attacks. Besides, most IDSs do not consider the imbalanced nature of ICS datasets, thereby suffering from low accuracy and high false positive on real datasets. In this paper, we propose a deep representation learning model to construct new balanced representations of the imbalanced dataset. The new representations are fed into an ensemble deep learning attack detection model specifically designed for an ICS environment. The proposed attack detection model leverages Deep Neural Network (DNN) and Decision Tree (DT) classifiers to detect cyber-attacks from the new representations. The performance of the proposed model is evaluated based on 10-fold cross-validation on two real ICS datasets. The results show that the proposed method outperforms conventional classifiers, including Random Forest (RF), DNN, and AdaBoost, as well as recent existing models in the literature. The proposed approach is a generalized technique, which can be implemented in existing ICS infrastructures with minimum changes.