An analysis is presented of a public-private partnership model in the natural resources sector of Russia, whereby the government provides tax incentives and supports the investor in infrastructure development and, to some extent, in the implementation of mandatory environmental measures. The analysis builds on the Stackelberg model and an original iterative solution algorithm based on probabilistic local search. A full-size model test site is constructed to demonstrate the capabilities of the approach. The actual data and dimensions of the model test site capture the specificity of the modeled object and make possible a practical study of the properties of the Stackelberg equilibrium. Based on the modeling results, an assessment is made of the impact of various factors on the effectiveness of the subsoil development program and the basic principles are formulated for government decision-making in this area.