On Tuesday, a church assembly in the capital Tallinn adopted new statutes of its own, which stipulate independence in the administrative, economic and educational areas, as stated on the website.
The name of the church was also changed and now reads "Estonian Orthodox Church" - the addition "of the Moscow Patriarchate" was removed.
Previously, the Estonian government had emphatically demanded the complete separation of the Estonian Orthodox Church from Moscow because the patriarchate there, which is loyal to the Kremlin, openly supports Russia's war of aggression against Ukraine.
The head of the Estonian church, Russian citizen Metropolitan Eugeni (Reshetnikov), had to leave Estonia in February because the authorities refused to renew his residence permit. He therefore chaired the meeting via video link, according to media reports.
According to the church, further negotiations with the state were also approved at the meeting.
Unification?
The talks with the government are about uniting the Estonian Orthodox Church with the Estonian Apostolic Orthodox Church, which belongs to the Ecumenical Patriarchate of Constantinople.
The church only commented on this indirectly in its statement, saying that the meeting was confident "that the Orthodox in Estonia will succeed in finding ways and means to heal the schism on the basis of canon law, mutual respect and equality".
She also emphasised: "On the 33rd anniversary of the restoration of the independence of the Republic of Estonia, we pray for the prosperity of Estonia as a sovereign state and for the preservation of its culture, traditions and freedom."
Daniel (Lepisk), an ethnic Estonian who was consecrated bishop of Tartu and vicar-bishop of Tallinn at the beginning of February, was recently the main figure in the Estonian Orthodox Church.
At the urging of the government, Daniel met with a representative of the Ministry of the Interior on 30 July.
Both sides agreed on further steps to reduce and eliminate the influence of the Moscow Patriarchate on the Estonian Orthodox Church, according to a statement from the Ministry of the Interior.
Bishop Daniel said on Estonian television at the time that consultations between the country's two Orthodox churches could begin in the autumn.
The head of the Estonian Apostolic Orthodox Church, Metropolitan Stefanus, had declared that his church was open to seeking a good solution that would satisfy all sides.
In Estonia, the majority of the population does not belong to any religious community.
In the 2021 census, 16 per cent of citizens professed Orthodox Christianity - no distinction was made between membership of the two Orthodox churches.
The Lutheran Church followed in second place with eight per cent.