The situation which developed in the end 90ies in the post-Soviet territory and associated with the visible rise of the terrorist and extremist activity, increased the risk to the national security for the young sovereigns forced to take a fresh look at the system of the international relations. It became obvious that the terrorist and extremist underworld got the features of the organized transnational activity.
The heads of the law-enforcement authorities, who gathered at the Council of the Ministers of Interior on October 1, 1999 in Kiev, addressed the Heads of the States and Heads of the Governments of the CIS member-states noting that "…Rise of the terrorism, gangsterism, kidnapping, arms and ammunition trafficking, other grave offences seriously undermine the security of our states. Today escalation of violence takes place in the Caucasus and Central Asia, tomorrow it may spread over other regions. Under such conditions we have to offer fitting rebuff to the international terrorism, armed separatism and other acts of extremism, to consolidate the efforts of our countries and first of all their law-enforcement structures".
The CIS member-states came to understanding of the necessity to adopt political and legal decisions with regard to consensus subregional counter-terrorism policy, as well as respective management and organizational decisions.
Irrespective of the specificity of national-state structure and foreign and domestic policy, the states agreed that the Commonwealth should solve the fundamental issue of shaping a common doctrine of counter-terrorism security and its coordinated implementation while maintaining a due regard of their national interests
The necessity of creating a structure which would ensure coordination of the security bodies, special services and law-enforcement authorities in combating terrorism and other violent acts of extremism was placed on the agenda of the Council of the CIS Heads of States. And this task has been solved.
On January 25, 2000, the Council of the CIS Heads of States met in Moscow and instructed the Security Council of the Commonwealth member-states together with the Council of the Heads of Security Bodies and Special Services, Council of the Ministers of Interior, Council of the Defense Ministers of the CIS member-states to elaborate a target program of combating international terrorism and extremism having envisaged inter alia establishment of a common antiterrorism center.
The panel discussion of the issue demonstrated that the parties supported the idea of establishing an Antiterrorism center under the leadership of the Council o f the Heads of Security Bodies and Special Services of the CIS member-states.
The Decision of the Council of the CIS Heads of States of June 21, 2000 held in Moscow established the Anti-Terrorism center of the Commonwealth of Independent States and approved its Regulation.
Lieutenant General Boris Alexandrovich Mylnikov was appointed the first Head of the CIS ATC (from November 2000 to November 2006).
Colonel General of Police Andrey Petrovich Novikov has been heading the CIS ATC since 2006.