The Eastern Orthodox Church in the newly independent Estonia — the second act of the controversy

In 1993 the Churches and Congregations Act was passed in Estonia. According to the new law, churches, congregations and religious associations were to re-register their statutes in the Ministry of Internal Affairs. In August 1993, the 1935 EAOC statute was registered by the Ministry according to which the EAOC had maintained legal continuity in emigration. In November, the same year, Bishop Kornily, who had earlier entered the church of which he was the leader in the Registry of Business Companies, Institutions and Associations, submitted the 1935 church statute for registration under the name of Estonian Apostolic Orthodox Church. The Ministry of Internal Affairs refused to register the church of the same name, referring to the law. Bishop Kornily took the case to court trying to prove the historical and judicial continuity of the Church under his leadership with the pre-Soviet EAOC. The allegations of Bishop Kornily were not proved in court and the EAOC became now subject of property reform.

Throughout the 1990s, the ROC and the Russian authorities accused Estonia of discriminating against the Russian-speaking Orthodox believers as well as the Russian minority, bringing as an example the refusal of the Estonian authorities to recognise the Russian Orthodox Church under the leadership of Bishop Kornily. However, the reports of the US State Department and Freedom House on religious freedom, did not confirm the accusations of discrimination on a religious basis in Estonia. Russia linked the improvement of Estonian-Russian economic relations with the registration of the ROC under the Moscow Patriarchate as the legal successor of the EAOC. It should be noted, however, that the real source of the dispute was legal continuity — the issue of expropriated buildings and lands — who will own them and to whom they will be restored.

During the 1990s official and unofficial talks were held between the Estonian authorities and the representatives of Bishop Kornily on the question of registration of the Orthodox Church of the Moscow Patriarchate. In the 1990s the entries of one Russian Orthodox convent (1997) and one congregation (1999) into the registry of Estonian churches and congregations were announced. This gives sufficient grounds to allege that the ROC was not persecuted in the 1990s. The refusal to register the Church was, above all, a legal question.

In 1996 Patriarch Bartholomew of Constantinople restored the 1923 tomos (it had been annulled for Estonian territory, but not outside of it), according to which the EAOC fell within the jurisdiction of the Constantinople Patriarchate. This fuelled the conflict and the Moscow Patriarchate broke off relations with the Constantinople Patriarchate. The interests of these two patriarchates clashed not only in Estonia but in other former Soviet-bloc countries, as both regarded them as their canonical territory. The only compromise reached by the two patriarchates was that the congregations in Estonia were permitted to choose themselves to which parish they wanted to belong. The majority of Orthodox congregations in Estonia chose the EAOC. However, even as late as 2000, the Council of the ROC Archbishops did not recognise the EAOC or its jurisdiction within the Constantinople Ecumenical Patriarchate. In the same year, Patriarch Bartholomew made a historic visit to Estonia and suggested that the Moscow Patriarchate replace the local church leader Kornily.

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