The usage of integrated indicators is an essential characteristic for development program implementation of Russian higher education, including the competitiveness improvement program. The competitiveness improvement program is a project of the Government of the Russian Federation aimed at significantly increasing the competitive position of leading Russian universities in the global market for educational services and research programs (Project 5-100). Different groups of program participants face different positive and negative aspects of this management tool. One of the risks bound up with focusing on indicators is often called the mismatch of the indicator system focused on the international model of universities, and the role of universities as drivers for the regions’ development and sectors of the Russian economy. This risk requires a systematic assessment. The purpose of this study was to systematize the events of changing and using the indicator system in the program at various levels of management, taking into account the general context in which the program is implemented, to compare them with the indicators of individual universities and create an information basis for further comparison with university practices. Two universities of the 5-100 program, which have a strong tradition of working with both basic and high-tech industries, were selected as reference universities for a preliminary analysis. An important part of this study apparatus was the historical comparison method of changes in the indicator system in dynamics.