The evolution of the Industrial Internet of Things (IIoT) introduces several benefits, such as real-time monitoring, pervasive control and self-healing. However, despite the valuable services, security and privacy issues still remain given the presence of legacy and insecure communication protocols like IEC 60870-5-104. IEC 60870-5-104 is an industrial protocol widely applied in critical infrastructures, such as the smart electrical grid and industrial healthcare systems. The IEC 60870-5-104 Intrusion Detection Dataset was implemented in the context of the research paper entitled "Modeling, Detecting, and Mitigating Threats Against Industrial Healthcare Systems: A Combined Software Defined Networking and Reinforcement Learning Approach" [1], in the context of two H2020 projects: ELECTRON: rEsilient and seLf-healed EleCTRical pOwer Nanogrid (101021936) and SDN-microSENSE: SDN - microgrid reSilient Electrical eNergy SystEm (833955). This dataset includes labelled Transmission Control Protocol (TCP)/Internet Protocol (IP) network flow statistics (Common-Separated Values (CSV) format) and IEC 60870-5-104 flow statistics (CSV format) related to twelve IEC 60870-5-104 cyberattacks. In particular, the cyberattacks are related to unauthorised commands and Denial of Service (DoS) activities against IEC 60870-5-104. Moreover, the relevant Packet Capture (PCAP) files are available. The dataset can be utilised for Artificial Intelligence (AI)-based Intrusion Detection Systems (IDS), taking full advantage of Machine Learning (ML) and Deep Learning (DL).