The term Cloud computing is not new anymore in computing technology. This form of computing technology previously considered only as marketing term, but today Cloud computing not only provides innovative improvements in resource utilisation but it also creates a new opportunities in data protection mechanisms where the advancement of intrusion detection technologies are blooming rapidly. From the perspective of security, Cloud computing also introduces concerns about data protection and intrusion detection mechanism. This paper surveys, explores and informs researchers about the latest developed Cloud Intrusion Detection Systems by providing a comprehensive taxonomy and investigating possible solutions to detect intrusions in cloud computing systems. As a result, we provide a comprehensive review of Cloud Intrusion Detection System research, while highlighting the specific properties of Cloud Intrusion Detection System. We also present taxonomy on the key issues in Cloud Intrusion Detection System area and discuss the different approaches taken to solve the issues. We conclude the paper with a critical analysis of challenges that have not fully solved.