High responsibility and a wide variety of technological, design and project tasks are characteristic features of the machine-building enterprises of the space industry. The required product quality is achieved by automating engineering using computer hardware and software. The paper proposes complex system models for comparative evaluation of the effectiveness of the computer equipment allocation for the company units and controls the efficiency of their operation. The technique of using model of data envelopment analysis, aimed at both the identification of inefficient units and the definition of measures for the rational allocation of computer equipment, is proposed. A linear programming problem is formulated for a preliminary assessment of the use the computer technology in units. A mathematical model for constructing an efficiency practical frontier is proposed. The discrete programming problem for optimal computer equipment allocation is solved. Verification of the obtained solutions of the optimization problem is carried out using a simulation model based on the Petri net. The results of experimental studies are presented that confirm the adequacy and effectiveness of the proposed models.