We provide a nonlinear model of intersectoral balance with constant elasticity of substitution (CES) production functions of industries and CES utility function of final consumer for the study of intersectoral linkages in the Kazakhstan economy. The model is formalized in terms of the primal problem of resource allocation and the corresponding Fenchel dual problem which solution gives costs of inputs of industries in a supply network. We identify the model with the actual data of the Input-Output tables of Kazakhstan and estimate the elasticity of substitution of production factors for the aggregated industry complexes. With the help of developed framework, we evaluate the inter-industry financial flows in the aggregated supply network for the period 2013–2020 and compare the results with the actual data of Kazakhstan. The developed framework can be used to support decision-making processes in sustainable supply chain management in a situation of the government economic policy change and external shocks. Using the developed framework, we evaluate the risks for Kazakhstan’s supply chains in scenario of sharp weakening of the national currency.