An acceptable level of economic security can be achieved with a mechanism of adaptation to negative manifestations of macroeconomic instability and the creation of conditions to overcome sectoral sanctions in line with the priorities of industrial development. The results show that the main causes of the steady decline in the share of the manufacturing sector is foreign trade policy. Present trends of lowering import duties could lead in the medium term to growth of imports of manufactured goods, which should be considered in the context of economic security. In this regard, the implementation of the import substitution policy assumes that the structure of industrial production will increase the share of consumer demand. It is especially difficult, due to the presence of a stable inertial trend in engineering, to provide rapid growth in the sectors of investment demand. The simulation results based on the modified Grossman–Helpman model demonstrate that the hypothesis about the dependence of the size of the import tariff on the strength of industry lobby groups is not confirmed. Thus, the Russian foreign trade policy on tariffs is fragmented and does not form a set of common principles and priorities to support the key sectors of the manufacturing industry. In this regard, the main task is the formation of universal tools to increase the level of adaptability of businesses to the high volatility of endogenous and exogenous factors negatively influencing the level of economic security of industrial complexes. Otherwise, economic stagnation and the extension of sectoral sanctions can to preserve, and in case of a negative scenario to critically reduce the level of economic security.