The much-trailed Holy and Great Council meeting of the Orthodox Churches – billed as a Pan Orthodox Council but failing to secure the attendance of four of the 14 self-governing Churches – has concluded with resounding affirmations of unity and calls for the protection of Christians in the Middle East.

The council, years in the planning, was hit before it began by the withdrawal of four Churches, most prominent among them the giant Russian Orthodox Church, though they had previously signed up to all the council's agenda and preliminary documentation.

However, theologians and bishops were adamant that it retained its authority for the Orthodox world and its decisions will now be considered by all the Churches, including those that were not represented. The text of the final encyclical has been prepared with one eye on those who objected to its terms of reference, or even to its being held at all. It is firmly conservative in its theological tone, while it addresses some of the issues around globalisation, scientific advances and moral issues in similar terms to previous statements by Pope Francis. 

The official encyclical released on the council's conclusion contains a robust assertion of the Orthodox Church as the "authentic continuation of the one, holy, catholic and apostolic Church", making pointed reference to the Church councils that condemned Protestantism and the move to unite with the Roman Catholic Church, all of which are accepted as authoritative though none were attended by all Orthodox Churches at the time.

It also speaks of the need for "The re-evangelisation of God's people in contemporary secularised societies, as well as the evangelisation of those who have not yet come to know Christ" as "the unceasing duty of the Church".

Of the "contemporary crisis in marriage and the family", it says it is "a consequence of the crisis of freedom as responsibility, its decline into a self-centered self-realisation, its identification with individual self-gratification, self-sufficiency and autonomy, and the loss of the sacramental character of the union between man and woman, resulting from forgetfulness of the sacrificial ethos of love". It says that rather than just being a contractual relationship, it is "a Church-nurtured workshop of life in love and an unsurpassed gift of God's grace".

While the statement claims that "The identification of the Church with conservatism, incompatible with the advancement of civilization, is arbitrary and improper," it warns of the risks of unchecked scientific progress, particularly in the realms of biology and neuroscience. "Man is experimenting ever more intensively with his own very nature in an extreme and dangerous way," it says. "He is in danger of being turned into a biological machine, into an impersonal social unit or into a mechanical device of controlled thought."

The encyclical also addresses the problems of globalisation and nationalism, warning against the erosion of different countries' cultural traditions and their replacement by an "ideology of globalisation" which destroys societies in the name of economics.

In spite of the absence of the Syria-based Church of Antioch, which refused to attend because of conflicts over jurisdiction, the council made a strong plea on behalf of Christians in the Middle East. "The Orthodox Church is particularly concerned about the situation facing Christians, and other persecuted ethnic and religious minorities in the Middle East," it said. "In particular, she addresses an appeal to governments in that region to protect the Christian populations – Orthodox, Ancient Eastern and other Christians – who have survived in the cradle of Christianity."

In a section evidently aimed at reassuring conservatives in the Churches who are unhappy about ecumenical dialogue with other confessions – a key concern of the Georgian Church, which refused to attend – the council defended ecumenism on the grounds that,"Through this dialogue, the rest of the Christian world is now more familiar with Orthodoxy and the authenticity of its tradition." However, it continued, "It also knows that the Orthodox Church has never accepted theological minimalism or permitted its dogmatic tradition and evangelical ethos to be called into question."

A Russian Orthodox Church spokesman said it would consider the final documents next month. In a statement to Interfax-Religion, Archpriest Nikolay Balasho – pointedly avoiding calling the gathering in Crete a council – said: "I believe that the Russian Orthodox Church's Holy Synod at its next meeting, which is usually held in July, will consider the documents of the assembly of hierarchs and representatives of 10 local Churches, which was held on Crete, in order to express Moscow Patriarchate's attitude to them."