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Although the National Archives as an institution is young, the establishment of the national archives system started already at the beginning of the Republic of Estonia. Due to the Archive Committee’s first discussions on March 3 in 1920 and their initiative, the current Historical Archives was established in Tartu as the holding place for historically significant insitutions records and the State Archives in Tallinn as the keeper of records of active institutions. The 1935 Archives Act strengthened the role of archives in the preservation and usage of society’s valuable records. During the Soviet occupation the archives continued their work, the regional archives, which were active in larger towns, were renamed as city archives and governed by Moscow. Independent management of the archives was restored in the 1990s and the National Archives of Estonia became active on January 1, 1999, in accordance with the Archives Act passed in 1998.

Since 2012, the National Archives acts on the basis of a renewed Archives Act as well as Archival rules.