The article considers the strategies and mechanisms of adaptation of the agro-industrial complex of Siberia to new conditions of the economy in transition, generated and transmitted by the Interregional Association “Siberian Accord”. Some of its main activities are the development of institutions and mechanisms of cooperation among regions, the exercise of influence on the central authorities to adjust policies on agriculture, and the elaboration of projects and programmes of interregional cooperation. The conclusion drawn is that under the pressure of ideology and conducted reforms, which led to the destruction of economic ties and the deficit of investment in the regions, within the association, approaches were transformed as to both the ideological basis of reforms and particular mechanisms of their implementation. The idea of regional self-sufficiency and sustainable use of local resources soon was transformed into the demand for introducing regulatory mechanisms in the form of special state regional policy in which a significant part was to be played by regional authorities. As to the organization of industrial interaction, initial plans for the creation of associations of Siberian manufacturers were replaced by objectives for the organization of joint stock companies ultimately transformed into the idea of organizing federal state joint stock corporations. In the course of implementing these practices a new form of interaction between the centre and the regions was created based not on the “vertical of power” as it was before, but on a dialogue of different levels of power that allowed taking regional interests into account.