Subject. This article deals with the control and management aspects of regional development on the basis of Leontief’s balance model. Objectives. The article aims to develop schemes for stable estimation of aggregate parameters of region balance models based on a shortened sample of input-output statistical data and rules for their subsequent regularization. Methods. For the study, we used multiple forms of regional economic balance model transformation based on the aggregation of data of the selected regional subsystems. Results. The primary estimates of aggregate input-output matrix for the southern regions of the Tyumen Oblast were obtained from the statistical input-output data for 2014–2018. To comply with the productivity conditions, additional information was introduced into the estimation algorithm reflecting the balance dependence for the reference input-output matrix for the Russian Federation and for the southern regions of the Tyumen Oblast in retrospective (2004–2013). Conclusions. The result of regularization of aggregate input-output matrix for the southern regions of the Tyumen Oblast obtained from the statistical input-output data on the basis of the least squares method indicates that the backward estimation technique cannot act as a basic tool for the primary construction of balance models of regional economies. However, backward estimation algorithms with subsequent regularization are effective in correcting the reference input-output matrix using actual data of the region’s socio-economic development.