Since 1997 till 2001, the post of the Director of the KazISS was held by leading scientists, famous political and social public figures of Kazakhstan L. Y. Tarakov (Chief Editor of the “Vremya” political newspaper), А. К. Sultangaliyeva (famous Kazakhstani orientalist, author of monographies devoted to Islam), Е. К. Yertysbayev (Extraordinary and Plenipotentiary Ambassador of the Republic of Kazakhstan in the Republic of Belarus) and М. S. Ashimbayev(First Deputy Chairman of Nur Otan party), who notably contributed to development of the Kazakhstan Institute for Strategic Studies under the President of the Republic of Kazakhstan.
Issues of outdoor and internal security in terms of new international conjuncture, regional relations system and major trends of economic development were in the foreground of scientific researches. Thus, large emphasis in the KazISS researches of that period was placed on development of multiparty system, appraisal of place and role of opposition, development of parliamentarism, which was stipulated by domestic political development of Kazakhstan, related to results of the constitutional reform of 1998. The KazISS became a dialogue platform for authorities and opposition spokesmen. During that period the KazISS carried out substantive work during election campaign for the first contested elections of the President of the Republic of Kazakhstan dated 1999, where N. A. Nazarbayev obtained the majority of voices among 4 candidates - 81,75%.
Much attention shifted to Islamic studies, which is still relevant in the KazISS researches nowadays on the context of analysis of terrorism and extremism threats. Cooperation with the Security Council of the Republic of Kazakhstan was enhanced with the advent of M. S. Ashimbayev (Director of the KazISS in 2000-2002, was concurrently leading the Analytical Center of the Security Council of the Republic of Kazakhstan).
During that period, the Institute strengthened its position in the area of public analytics. The “Kazakhstan and the world society” magazine was rebranded and published under the “Kazakhstan-Spectrum” title since 1997. М. М. Tazhin (Deputy Head of the Presidential Administration of the Republic of Kazakhstan), L. Y. Tarakov (the KazISS Director), U. Т. Kassenov (the KazISS First Director), B. R. Akhmetgaliyev (the KazISS consultant) were included into the first editorial board.
At the end of 1999, the KazISS established a new analytical magazine called “Analytic”; its first issue contained the interview with N. A. Nazarbayev. The Head of the state considered issues of regional security, the Afghan problem, legal status of the Caspian Sea, the UN operation, and other in details. At the end of the interview the President emphasized significance of the KazISS scientific activities related to the issue of conducting fundamental researches on key problems of foreign and internal policy of the country.
In 2001, the Institute drew up the “Virtual image of the KazISS under the President of the Republic of Kazakhstan” project, aimed at promotion of scientific and research activity of the Institute by means of the official website.
The Institute continued to establish international contacts actively. The start of the KazISS cooperation with the Fund named after F. Ebert in April 2001 was marked by a joint conference devoted to religious extremism problems in Central Asia. The Institute strengthened contacts with foreign research centers, such as the Shanghai Institute for International Studies, the Institute for Defence Studies and Analyses (India), the Institute for Strategic and Interregional Studies under the President of the Republic of Uzbekistan, the Russian Institute for Strategic Studies, etc. Such cooperation is being actively pursued nowadays. One of its formats is conducting expert meetings. Thus, in the summer of 2017, the KazISS venue held a regular expert meeting with representatives of the Shanghai Institute for International Studies, where relevant issues of cooperation between the Republic of Kazakhstan and the People's Republic of China were discussed.
Within the period between 1997 and 2001, the KazISS continued to accumulate experience of research practices based on domestic and international agendas of that period.