The religious leaders celebrated Orthodox Pentecost in the town of Heraklion on Crete where a "divine liturgy" was given as part of the gathering that will last until June 27.
Ecumenical Patriarch Bartholomew called the so-called Holy and Great Council on issues including wedlock, fasting, and united representation in dioceses in countries such as the United States and Australia.
Greek President Prokopis Pavlopoulos took part in the mass that was aired live on state broadcaster ERT.
Aside from Russia, the Orthodox churches of Bulgaria and Georgia are also absent. Both are considered close to Moscow.
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The Patriarchate of Antioch is also staying away because of a spat with Jerusalem over the appointment of clerics in Qatar.
"This great and holy council will carry the message of unity... It will help to escape the deadlocks of the present," Patriarch Bartholomew of Crete told local media.
"The unity of Orthodoxy is good for us all. It is those who are absent who will miss out," said Greek Foreign Minister Nikos Kotzias.
The Orthodox communion has about 250 million followers worldwide and consists of 14 autonomous churches though it has been shaken by the upheavals in the former Soviet bloc and the Middle East in recent decades and is frequently plagued by national and political strife.