In 1941 Hitler invaded the Soviet Union, and in the same year the Romanian and German occupation of the Ukraine led to the 1941 Odessa massacre in Naimark's hometown. Naimark joined special duty (called "home-guard") during the war and worked on the labor front, moving to Tashkent with the Seismological Institute at the end of 1941 as the Nazi army advanced on Moscow, where he remained until 1943.