In a virtual networked system where infrastructure is shared by more than one user security is a serious concern. Good network security protects a network in a manner that is consistent with its purpose and precautions must be taken when choosing a network provider for an organization. An attacker can enter into the system and compromise virtual machines and then exploit vulnerabilities. During the packet flow through the network experiences some delay. The existing intrusion detection processes incorrectly identify this delay as intruder's attack. This work is intended to efficiently identify the intruders in the case of congestion and find possible countermeasure using Intrusion detection manager (IDM) in virtual networked system. The Intruder Detector and Manager (IDM) algorithm detects and prevents the intruder entering into the network by maintaining tables and reconfigurable virtual network-based countermeasures in order to avoid the masquerading DDoS attacks. When this procedure is followed, IDM increases the throughput by preventing intruders and maintains the history of intruders.