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 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 meeting of the Council of the Ministers of Interior on October 1, 1999 in Kiev, addressed the Heads of States and Heads of 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 necessity of founding a structure which would ensure coordination of the security agencies, special services and law-enforcement authorities in combating terrorism and extremism was included in the agenda of the Council of the CIS Heads of States.
On January 25, 2000, the Council of the CIS Heads of States met in Moscow and exchanged views on how to combat international terrorism amid the outcomes of the OSCE Istanbul summit.
This meeting instructed the security councils of the Commonwealth states in cooperation with the Council of the Heads of Security Agencies and Security 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 joint antiterrorism center.
The Council of the CIS Heads of States which met on June 21, 2000 in Moscow adopted a decision to establish the Anti-Terrorism Center of the Commonwealth of Independent States and approved its Regulation.
The decision of the Council of the CIS Heads of States as of October 7, 2002 founded the CIS ATC’s representative office for the Central Asian region to be located in Bishkek, Kyrgyz Republic.