Advanced Persistent Threat (APT) has recently emerged as sophisticated and tailor-made attacks. APTs pose threats mainly targeting military, defense, security infrastructure, high profile companies, and government units. Intrusion detection mechanisms are crucial for adequate protection, especially as a countermeasure for APT attacks done by hacktivists, cyber warriors, and cyber terrorists over management information systems (MIS) of government institutions and e-government applications. In this study, Intrusion detection and prevention systems have been studied in detail after being referred to the tasks and abilities of the intrusion detection systems that are at the core of the computer security technology presented today to meet the increasing need for information and network security. This paper aims to specify the differences between Host Based Intrusion Detection Systems (HIDS) and Network-Based Intrusion Detection Systems (NIDS) and compares the tools using HIDS and NIDS. It is asserted that to better assurance for APT attacks, there should be a Hybrid IDS approach covering both networks and hosts using both signature and behavioral detection mechanisms based on deep learning algorithms.