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The article reviews the historic experience in forming the regional Executive Authority during the 1990-ies of the XXth century in the Kemerovo, Novosibirsk and Tomsk regions. The 1990-2000 period, which is marked with establishing and developing the new Russian statehood on the basis of the concept of separation of powers, can be divided into two main periods of establishing the regional Executive Power in Russia, i.e. 1990-1993 and 1994-2000. Each period has had a decisive influence on formation of governance institutions both in regions and in the country as a whole, and is characterized with significant changes in principles of interaction between the Russian Federation and its constituent entities, and between the legislative and executive branches of Government. The first period, 1990-1993, covers the formation of Executive Authorities that were formed on the basis of concepts of Soviets sovereignty and of separation of powers including reauthorization of Legislative and Executive branches of Government. During this period the development of regional governance systems coordinated by Executive Bodies was retarded by the total disorder, uncertainty and instability of the Russian Authority and Governance Systems. During the second period, 1993-2000, concepts of separation of powers and authority matters between the Center and regions of the country became the background for formation of the Executive Authority. This period is characterized by formation of the vertical of Executive Power in the country and by the tendency towards centralization of the administration activities in regions.