After the incorporation of the Baltic region into the Soviet Union in 1940, a diverse process of Sovietisation was launched in the new Soviet republics, which also affected administrative division. Major changes were not undertaken during the first year of Soviet occupation, yet in the course of the re-occupation of Estonia in 1944–1945, the borders of the union republic were altered: the territory east of Narva was made part of Leningrad oblast and most of Petseri County, including the town of Petseri, was added to the newly created Pskov oblast. The former Petseri County was done away with and the parts of it that were left were added to Võru County. The existing administrative division was initially preserved after the war as well. In 1945, the Estonian SSR consisted of 10 counties and 236 rural municipalities. Later the separate counties of Hiiu (1946), Jõhvi and Jõgeva (1949) were created. Additionally, village soviets were established in the rural municipalities in 1945 as first (local) level authorities.

Gradually, however, comprehensive administrative reform was prepared. The first plans, which called for the division of the Estonian SSR into about 40 raions, had been completed by the summer of 1949 at the latest. Risti, Kuusalu, Võnnu, Veriora or Tõstamaa could also have become the hubs of raions. Some later raions, like Kiviõli, Kallaste, Pärnu-Jaagupi or Türi, were not in the initial plans. The new administrative division was announced on 26 September 1950 with the act ‘Concerning the formation of rural raions in the Estonian SSR’ issued by the Presidium of the Supreme Soviet of the Estonian SSR, which did away with counties and rural municipalities, and divided the Estonian SSR into 39 rural raions and five cities ‘subordinated to the republic’. In terms of both territorial size and number of inhabitants, the largest raion was Jõhvi and the smallest was Otepää.

As first level administrative units, there were too many raions. The oblasts of Tallinn, Tartu and Pärnu were created in the Estonian SSR in 1952, but they were already done away with the following year. The merging of raions began in 1957 when Loksa raion was eliminated. In 1959, 13 raions were already done away with, and another two were eliminated in 1961. The creation of territorial kolkhoz and sovkhoz administrations in 1962 became the basis for the final reduction in the number of raions. For the first time in history, it prescribed the division of Estonia’s territory into 15 administrative units. In that same year, the number of raions in the Estonian SSR was also reduced to 15. The last raions to be done away with were Abja, Elva, Märjamaa, Põltsamaa and Vändra. The borders of raions were altered later on as well, yet their number remained constant until raions were eliminated after the restoration of Estonia’s independence.

It appears from the archival records of the liquidation commissions that the reorganisation of the raions came relatively unexpectedly for the local Communist Party elite and it was carried out hurriedly. The wishes and intentions of the local people were also listened to in the course of the reorganisations. Almost without exception, the people wanted to join a larger centre. If the opinion of the people diverged from the general principles for establishing raions, it was discarded. In the course of doing away with raions, hundreds of employees of the Party apparat and that of the local soviets were dismissed from their posts. The jobs that were offered to them were obviously at a lower position than their former posts. Two Party Committee functionaries and two Komsomol Committee functionaries were among the six Abja raion employees for whom no new jobs whatsoever could be found.

Comparing the reorganisation of raions in the Estonian SSR and the Latvian SSR, we see similar features. The average size of raions was similar in Estonia and Latvia. Raions were considerably smaller in the Lithuanian SSR.