The article is devoted to the topical issues of the program based method of cooperation management processes in the CIS. It provides an overview of global experience in the development and implementation of international programs. There are offered their possible classification criteria and analysis of currently existing preparation and execution mechanisms of international programs and the direction of their improvement in CIS. The aim of the article is to discover deficiencies of the organizational process, to explore methodology "blank spots" оf the CIS regulations and to propose adequate solutions. The main conclusion is that the active procedure hampers CIS integration, and it has to be reworked. This article was prepared on the basis of HSE research in the development of the "Interstate program of innovation cooperation among the CIS up to 2020," adopted by the CIS Heads of Government Council, October 18, 2011.