During the first half of the 1940s, the political situation changed several times in Estonia: from the loss of independence in June of 1940, followed by the first Soviet occupation from the summer of 1940 to the summer of 1941, which was replaced by the German occupation from July of 1941 until the autumn of 1944, returning again to Soviet occupation. Along with the reshaping of Estonian society at large, these years also saw some attempts at reorganising local archaeology as well, although it was not as dramatic as the overall impact of totalitarian regimes on the fabric of society. This paper describes what kind of moves were planned by the new authorities, what the reaction of Estonian archaeologists was, and what the actual outcome was.

In all, plans specified the organisation of the former national science according to the rules of foreign authorities. By and large, the ideas of the Soviet and German occupying powers were similar: first of all, local archaeology had to use organisational models that were similar to those used in Soviet Russia and National Socialist Germany – fully centralised, ideologically controlled, and separating teaching from museum activities, since the latter was regarded important for ideological purposes. In reality, the first Soviet occupation (1940–1941) only managed to change the labels of organisations and had minimum impact on personnel. The German occupation was also too brief for profound alterations, but during those three years, a new person replaced the Professor of Archaeology. There were some minor changes at the organisational level but by and large, the reorganisation had minimal impact on daily activities.

When trying to analyse the impact of totalitarian ideology on Estonian archaeology during those years, it is possible to state that the effect was minimal at the research level since fieldwork and published papers followed the traditions established in the 1920s and 1930s. At a personal level, some archaeologists collaborated with the new authorities within the first months of Soviet occupation while others tried to distance themselves when possible or even tried to work against the new authorities, at least during the German occupation. In conclusion, Estonian archaeology remained relatively unaffected by totalitarian ideology at first, only to be completely restructured during the next five years.