The procedure of assessing the project’s influence on the environment during which, inter alia, the compliance of the implemented project (eg concerning technical infrastructure, linear investments, or processes that affect the forms of nature) with the requirements of the environmental protection is verified, constitutes an environmental management instrument. Especially the environmental authorities leading or consulting this procedure may apply different limits and concepts of the action. At the same time they are limited by legal determinants. The aim of this article is to identify the most significant organizational problems that have arisen during the application of this procedure at the level of regional directors of environmental protection throughout the country. As a part of the study to fulfill the aim of the research, an analysis of all cases conducted by them was carried out. This led to a dispute and a consequence in the form of an appeal against the issued decision on the environmental conditions and the outcome of the appeal by the Director General of Environmental Protection. This article has verified the substantive scope of the issues, the ways to resolve conflicts and their impact on the regional and national development. Based upon these results, the proposals for changes of the environmental management system have been formulated.