State development programs in Russia are important instruments of strategical planning and economic development. The article analyzes the institutional and methodological support of the implementation of government programs. The methodology of research is system approach. The purpose of research is identification of planning and implementation dysfunctions of state development programs in Russian Federation. Objectives of the study: the allocation of types of planning dysfunctions; characteristics of the planning dysfunctions on the example of the state program «Development of agriculture and regulation of markets of agricultural products, raw materials and food in Kostroma region for 2013–2020 years». Research methods: structural analysis of the passport and reports on the implementation of the state program of the Russian Federation; a comparative analysis of documents of legal and methodological support of planning and implementation of the state program. The article identifies and discloses the following dysfunctions of planning: 1) incomplete compliance with the goals, objectives of the program, the target set of indicators; 2) in the proposed target indicators of passports of the state programs are many dynamic parameters and few parameters characterizing the structure; 3) in the target indicators are not taken into account the ratio of growth rates of the subsystems of the economy; 4) lack of a system of target indicators for each management level (Federal, regional, local); 5) the non-substantiation of the target values; 6) ignoring the specifics of the regional economy; 7) the non-substantiation of the method of calculating the level of effectiveness of implementation of the state program. The paper gives a characterization of the dysfunctions of the following institutional systems: 1) inconsistency in legal requirements or the possibilities offered by the legislation (e.g. public programs), the structural conditions and financial resources of individual regions, municipalities, enterprises, etc.; and 2) dysfunction of non-compliance of formal institutions.