The Constitution of the Republic of Estonia stipulated that justice be administered by independent courts. District courts fulfilled the function of lower-level (first instance) general courts. Circuit courts dispensed justice at the second level. In 1940, there were four circuit courts in Estonia – the Tallinn, Viljandi, Tartu and Rakvere Circuit Courts. The highest-level court was the Supreme Court, which heard appeals. The Supreme Court would either concur with the decisions that had been adopted or send them back to the circuit courts.

Changes began in July of 1940, when senior judges as well as prosecutors were dismissed. On July 17, Acting Prosecutor of the Chamber of Courts Gustav Avald was dismissed, followed by the Prosecutor at the Supreme Court Johannes Müller on August 8, and the Chairman of the Chamber of Courts Jaak Reichmann on August 13 (since he had reached retirement age). Formal justifications were provided for their departure, such as their having reached retirement age, but also on grounds of health problems and because of personal reasons.
The replacement of judges had already begun during the puppet regime of Johannes Vares, but not on a massive scale. This continued in stages until June of 1941.
During the summer of 1940, the chairmen of the circuit courts were also replaced. The younger jurists who took their places were graduates of the Faculty of Law of Tartu University, and were individuals that the occupying power regarded as somewhat more trustworthy than their predecessors. There were many jurists in Estonia. It was possible to study at the Faculty of Law even if one was working at the same time. This was an opportunity used by many students who were not well off. In left-wing circles, it was not unusual for someone to have a degree in law, and the occupation forces recruited new cadre in these circles.
Political repressions were coordinated by operative groups of the NKVD of the USSR. To do this, they initially drew on rights given to the Chief of Internal Defense under conditions of Martial Law. They employed the political police, which was staffed by communists. Sentences now began to be passed by various tribunals and Special Councils, as designated by the Code of Criminal Justice of the Russian SFSR.
In 1940, the Estonian Supreme Court consisted of 16 Justices. The veteran Chairman of the Court Kaarel Parts died of natural causes on December 5, 1940, and another Justice also died during 1940. Six justices were imprisoned during the 1940–1941 period. They all perished in the prison camps. Two were arrested after the war. One Justice died while trying to escape across the Baltic Sea during the fall of 1944. Five Justices managed to avoid being arrested.
In 1940, the Chamber of the Courts and the four circuit courts consisted of 70 judges. 15 of them were arrested during 1940 and 1941. All of those arrested perished in the prison camps. Of these, six were shot or died before they were to be executed. One judge died while trying to escape across the Baltic Sea during the fall of 1944. After the war, an additional seven former judges were imprisoned.

The ESSR Constitution ratified on August 25, 1940 fixed the basis for a new, ESSR court system. Aleksander Jõeäär was appointed the People’s Commissar of Justice of the ESSR; Ferdinand Adamson, a former Estonian Red Army soldier who served in the Cheka and NKVD from 1929 to 1938, was named the head of the administration of judicial bodies.
On November 16, 1940 the reorganization of the judicial bodies according to the Soviet system was started. Accordingly divisional courts were reorganized into people’s courts, district courts into courts of the same name that deliberated judicial matters of the first- and second-degree. The Estonian Supreme Court was abolished. The appointment of District Court and Supreme Court members was confirmed first by the Bureau of the Estonian Communist Party Central Committee, and thereafter, they were “elected” by the December 31, 1940 decree of the ESSR Supreme Soviet.

On December 16, 1940, the Criminal Code of the Russian SFSR formally became valid in Estonia, which in practice had been true since the beginning of the summer. Retroactively, it was also applied to many cases that had taken place before July 21, 1940. Now members of the Supreme Court and District Courts were replaced with lawyers brought to Estonia from the Soviet Union. On March 31, 1941, Ivan Haritonov was named to be the First Deputy of the Chairman of the Tartu District Court; on April 28, 1941, Johannes Evertson was named Chairman of the Viljandi District Court, Bernhard Rosenbaum Chairman of the Rakvere District Court and Theodor Unt Chairman of the Tallinn District Court. In March and June of 1941, Ljudmilla Vallner and Aleksei Vassiljev were named to be members of the Tallinn District Court; in March 1941, Vassili Zaitsev was appointed First Deputy of the Chairman of the Rakvere District Court, as well as others. In June 1941, Leonid Jürgens was appointed Chairman of the Supreme Court and Vassili Gussev was named as a member; at the end of 1940, Aleksei Korotkov was named First Deputy of the Chairman of the Supreme Court. These judges were brought to Estonia from the Soviet Union. In April of 1941, Nadežda Tihhanova-Veimer (spouse of Arnold Veimer, ESSR Light Industry People’s Commissar), a spinner at a calico-printing works and figure in the workers’ movement who possessed no legal education, was named as a member of the ESSR Supreme Court.
The retroactive implementation of Russian laws and the passing of judgment in tribunals and Special Counsels made it possible to make people in the state service of the Estonian Republic, politicians, military personnel, public figures, members of social organizations, entrepreneurs, and farmers into potential criminals who were sent to prison camps or sentenced to death primarily on the basis of § 58 (counter-revolutionary crimes) of the Russian SFSR Criminal Code. The family members of those repressed were deported into the furthest hinterlands of Russia and Siberia.
Soviet ideologues based the repression of the residents of Estonia, as well as the other countries and territories occupied in 1939 to 1940, on the theory of “the intermediary period of counter revolution (this meant the independence period in Estonia, Latvia and Lithuania and the period that western Ukraine, western Belarus, northern Bukovina and Bessarabia were part of Poland, Czechoslovakia and Romania respectively) during the implementation of Soviet power.”

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