Introduction: When ensuring preparedness of constituent entities of the Russian Federation to take anti-epidemic measures in order to respond to imported infections, including the novel coronavirus disease, appropriate training of healthcare workers, specialists of bodies and institutions of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor) and non-medical specialists was important. The objective of our work was to improve methodological support of inter-agency collaboration in implementing activities on sanitary protection of the territories at border patrol checkpoints. Materials and methods: We analyzed reports on interdepartmental drills at Russian border patrol highway checkpoints, including those conducted within the preparation for 2018 FIFA World Cup, and regulations on the aspects of interdepartmental drills at international border crossing points. Results: We assessed completeness of implementation, organizational structure, content, and methodological aspects of interdepartmental cooperation in the course of drills at highway checkpoints and proposed a unified approach to conducting training with account for realities of checkpoint functioning and requirements for ensuring biological safety. The article provides recommendations for conducting drills on anti-epidemic measures to be taken when identifying a suspected case of a highly hazardous communicable disease at border patrol checkpoints.