Although the National Archives of Estonia started operating on 1 January 1999, the system of state archives was formed in the early years of the Republic of Estonia. On 3 March 1920, the Commission for Archives initiated the establishment of the Central State Archives in Tartu to preserve documents from historically important institutions, and the State Archives in Tallinn for documents from institutions that were still active.
During Soviet times, the archives were maintained but were restructured. At that time, the archives were controlled by Moscow.
The old structure was restored in the 1990s. According to the Archives Act adopted in 1998, the National Archives of Estonia started its activities at the beginning of 1999. The new structure included the Historical Archives in Tartu, the State Archives and the Film Archives in Tallinn, and 15 land archives all over Estonia. The structure of the National Archives changed in connection with the construction of the new main building of the archives. By 2017, the National Archives had structural units in Tartu, Tallinn, Rakvere and Valga.
The National Archives have made great efforts to digitise a large number of archival records which are available on its web page for digitalised archival sources, called Saaga.
