The Russian Orthodox Church has rejected a last minute appeal to attend what was deemed as the first meeting of fellow church leaders since 787.
Russia said it could not participate in the Holy and Great Council, on the Greek island of Crete, as not all churches will be present, BBC reported.
The churches of Antioch, Bulgaria and Georgia had previously refused to take part after disputes about the meeting.
The gathering, due to start on Sunday, has been 55 years in preparation.
Fourteen churches representing over 300 million faithful were originally invited.
According to experts, the decision by the Russian church, which represents some 100 million followers, highlights longstanding divisions among Orthodox Christians.
There is also a struggle for power between Russia and the Istanbul-based Ecumenical Patriarch of Constantinople, Bartholomew I, considered the spiritual head and “first among equals”.
The disagreements ranged from seating plans to efforts to reconcile with the Vatican.
There are 300 million Orthodox Christians, who are members of 14 national churches. The denomination split from western Christianity – Roman Catholicism – in 1054 amid disputes about the power of the Vatican.
Orthodox clergy are distinguished by their elaborate headgear and thick facial hair, which they wear because the Old Testament prohibits shaving.