Abstract <p>This article is devoted to the reconstruction of the evacuation process of the USSR Academy of Sciences in 1941–1942. The authors focus on the organizational and institutional problems caused by the emergency relocation of academic structures. The study was conducted using a wide range of sources, including a significant set of documents from the Archives of the Russian Academy of Sciences, which are being introduced into scientific circulation for the first time. It is noted that the Academy’s management system, which had been established by the early 1940s, was generally able to cope with the workload, but the emergency that arose during the evacuation from Moscow in October 1941 required the creation of an institution of commissioners endowed with a broad (though not always clearly defined) range of powers. The authors conclude that the “fragmentation” of power became the institutional prerequisite for the conflict between the President of the USSR Academy of Sciences, Academician V.L. Komarov, and the Vice President of the USSR Academy of Sciences, Academician O.Yu. Schmidt. Overall, the institutional structure of the USSR Academy of Sciences coped with the tasks of evacuation; however, the chain of events it triggered contributed to the further loss of independence of the USSR Academy of Sciences and its integration into the military–industrial complex.</p>