The article examines the peculiarities of the spread and counteraction of the new coronavirus infection in Russian penitentiary institutions. Special attention is paid to the issues of keeping suspects, accused and convicted persons in isolation, as well as related recommendations of the Supreme Court of the Russian Federation. The results of the study of the order and conditions of isolation in Russian penitentiary institutions, together with somatic indicators of the age and health of persons held in them, give grounds for reasonable alarm about the existence of increased risks of the spread of COVID-19. However, practice shows that timely sanitary and epidemiological measures taken by the state and special restrictions of a regime nature in isolation have restrained the spread of the disease. Conclusions are drawn about the need to change some provisions of the Criminal Code of the Russian Federation, the Criminal Procedure Code of the Russian Federation and the penal enforcement legislation to ensure the possibility of urgent correction of criminal policy and law enforcement in conditions of high readiness for natural and man-made emergencies.