In 1940, as a consequence of the Molotov–Ribbentrop Pact, Romania was forced to cede part of its territory to the Soviet Union, including Chișinău, where the Moldavian SSR was formed. The new authorities closed the institute of Kotsovsky. The institute was reopened when, after the outbreak of World War II, Chișinău was taken by the Axis forces. Kotsovsky continued his active scientific work during World War II. At this time, he published his work mainly in German and Austrian scientific journals.