The article analyzes the crisis period life of the Republic of Moldova, when the Covid-19 pandemic aggravated relations between state structures and the Orthodox Church. The priests of the Church opposed the government’s extraordinary measures to limit the spread of a viral infection: the churches’ closing, the church utensils disinfection introduction. The Church in the form of an ultimatum also opposed vaccination forcing, which was seen as a conspiracy against humanity. The author examines the aggravation reasons of relations between the State and the Church. First of all, the reasons are in the state policy immaturity of the religious-state relations, in the absence of the Church and power institution function definition. There is a lack of knowledge in society about the social role of religion and the Church. The tense atmosphere of the pandemic crisis conditions and the infodemic spread - unverified information, rumors and phobias - in the media had a negative impact on the conflict emergence between the Church and State leaders in the Republic of Moldova.