This article discusses the system of customs authorities in Kyrgyzstan, their customs functions and key tasks at the present stage of development of customs in the country. One of the most important functions of the Customs Service in the context of Kyrgyzstan's membership in the Eurasian Economic Union is to ensure the formation of the revenue side of the state budget through the collection of appropriate taxes and payments, according to the division of administration of the latter between tax and customs authorities. Analysis of the activities of the Customs Union of the Kyrgyz Republic for 2016-2020 showed a deterioration in the dynamics of taxes and payments collected by the customs authorities of Kyrgyzstan, which was caused, first of all, by the global coronavirus crisis, which led to significant restrictions on the foreign economic activity of states. At the same time, under the conditions of economic quarantine restrictions, the participation of the Kyrgyz Republic in the EAEU has become a certain buffer against the negative impact of a decrease in the inflow of indirect taxes and customs payments.