Y The main research question of the paper is related to the identification and analysis of the challenges that Croatian local units face during the crisis caused by the COVID-19 pandemic. First, the regulatory framework of the civil protection system was presented to determine a direction of research of organizational and functional adjustments of local units for effective crisis management. Empirical research was conducted using the data content analysis (legal regulations, strategic documents, soft law documents, and web sourced data). Research findings have shown that local units face challenges in the areas of political governance, administrative and professional affairs, local budget, and the implementation of local democracy mechanisms. Therefore, in each of the identified areas, the author has analyzed elements that are subject to adaptation to national recommendations to reduce the spread of coronavirus. In doing so, attention is focused on large cities and county centers and their adjustments during crisis management were analyzed.