This survey paper shows the state of the art in security mechanisms, where a deep review of the current research and the status of this topic is carried out. We start by introducing network coding and its variety of applications in enhancing current traditional networks. In particular, we analyze two key protocol types, namely, state-aware and stateless protocols, specifying the benefits and disadvantages of each one of them. We also present the key security assumptions of network coding (NC) systems as well as a detailed analysis of the security goals and threats, both passive and active. Current proposed security mechanisms and schemes for NC in the literature are classified too. This paper also presents a detailed taxonomy of the different NC security mechanisms and schemes reported in the literature.