In this paper, a method of identifying conflict relations between the subjects of business processes is presented. The proposed solution seems quite important due to the high sensitivity of modern high-tech enterprises’ business processes to negative factors, as well as the need to develop correct management decisions in conflict situations. A company’s ability to identify internal conflicts and to take them into account during management decision-making is a feature of an effective business process. Modern methods of conflict detection that are available for practical use are able to identify conflict situations only at the stage of open conflict. In this case, the impact of the conflict on the business process is already material and may lead to deterioration in the company’s performance. Unfortunately, existing methods have a significant disadvantage: they are not able to identify conflicts at an early stage, when the impact of the situation on the business process is not noticeable. An innovative approach based on analytical processing of survey-based data is proposed. This approach is able to identify hidden conflicts among employees of the enterprise. Identifying a conflict situation at an early stage makes it possible to manage conflict and reduce subsequent financial loss.