This article is devoted to development of agent-based modelling methods in the ar-ea of intergovernmental relations in multi-level states. It is done a survey of literature on topical problems of these processes in the context of reforms of the Russian Federation budget system, introduced in the beginning of 2000-th with support of the World Bank consultants. In the list of these problems there is a task of getting a balance between two functions of intergovernmental relations: function of inter-territorial fiscal equalization and function of fiscal incentives of economic development. This balance depends on a construction of intergovernmental relations system. Authors discuss a general scheme of intergovernmental relations on the horizontal and vertical directions, added their rela-tions with firms, where there are subjects of relations such as taxes, subsidies, transfers, pure and local public goods that cover different area. In particular, institutional condi-tions of economic activity are looked as public goods. It is suggested a system of agent-based models for intergovernmental relations research that includes: a model of inter-territorial competition for capital, labor, economic activity; a model of optimal configu-ration of administrative units; a model of vertical completion of governments in a multi-level state; a model of fiscal incentives for government to develop local economy (a mod-el of tax system system). Authors discussed two of these models in particular: the model of inter-territorial competition and the model of optimal configuration of administrative units, that have been implemented as computer programs on agent-based languages NetLogo и Jawa. Finally, authors suggested ways for development these models to solve tasks set in the article