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The growth of the Internet of Things (IoT) offers numerous opportunities for developing industrial applications such as smart grids, smart cities, smart manufacturers, etc. By utilising these opportunities, businesses engage in creating the Industrial Internet of Things (IIoT). IoT is vulnerable to hacks and, therefore, requires various techniques to achieve the level of security required. Furthermore, the wider implementation of IIoT causes an even greater security risk than its benefits. To provide a roadmap for researchers, this survey discusses the integrity of industrial IoT systems and highlights the existing security approaches for the most significant industrial applications. This paper mainly classifies the attacks and possible security solutions regarding IoT layers architecture. Consequently, each attack is connected to one or more layers of the architecture accompanied by a literature analysis on the various IoT security countermeasures. It further provides a critical analysis of the existing IoT/IIoT solutions based on different security mechanisms, including communications protocols, networking, cryptography and intrusion detection systems. Additionally, there is a discussion of the emerging tools and simulations used for testing and evaluating security mechanisms in IoT applications. Last, this survey outlines several other relevant research issues and challenges for IoT/IIoT security.