The troubled Pan-Orthodox Council is set to begin on Saturday in Crete, but without some key players. First envisaged 55 years ago, it was designed to bring together all of the 14 autocephalous or self-governing Orthodox Churches in the first such gathering since the 8^th century.

During the last fortnight it has been hit by last-minute withdrawals by Churches taking exception to the council's discussion documents, agenda and procedures. Most recently the powerful Russian Orthodox Church withdrew, calling for the council's postponement.

So can it still happen at all? And if it does, is it still a Pan-Orthodox Council, even if not all the Churches are there?

Yes and yes, according to Orthodox theologian Fr John Chryssavgis of the Greek Orthodox Archdiocese of America. Speaking to Christian Today, he said: "We are moving forward very smoothly with 10 Churches and we hope more will come by Friday. But the work is continuing with the clear mandate of all 14 Orthodox Churches."

Chryssavgis, one of Ecumenical Patriarch Bartholomew's advisers, admits it would be "tempting to say it is not Pan-Orthodox, if you look at the table and see there are three or four missing. But that was not how it was convened or conceived." Chryssavgis says that the process by which it was set up, with the agreement of the primates of the Churches and after a long process of discernment, means that its status as a Pan-Orthodox Council cannot be affected if some Churches withdraw. It's those Churches that are reneging on protocols that were previously agreed; it doesn't affect the essence of what will happen in Crete.

He confesses himself baffled by the last-minute criticisms and withdrawals, calling them "bizarre". All of the documents and procedures were agreed in advance, with every one of hundreds of pages initialed in every language of the council by every primate. "It is really surprising and perplexing," he says.

The dominoes began falling with the withdrawal of the Bulgarian Church, but the succession of criticisms and pull-outs reflect wider tensions in Orthodoxy between modernisers and ultra-conservatives. For some, Pope Francis' meeting in Havana with Patriarch Kirill, so much heralded in the West, was an unacceptable compromise with a communion they regard as heretical. Others protested the document on Orthodox relations with the rest of the Christian world, arguing that its emphasis on "restoring Christian unity" gave too much away. According to Bloomberg, rumours circulated among Russian Orthodox that the council was planning to allow bishops to marry and priests to remarry, to abolish monkhood and move to a common calendar.

And behind all this is the rivalry between Patriarch Kirill of the rich and powerful Russian Orthodox Church and Patriarch Bartholomew, hugely respected personally and first in prestige ecclesiastically, but with a fraction of Moscow's resources.

When Moscow pulled out it was ostensibly because it believed the council had ceased to be a valid one. "One Church after another declares that it is not participating, which means there will be no consensus, which means it is no longer a Pan-Orthodox Council," said the Russian Orthodox spokesman Metropolitan Hilarion.

Chryssavgis disagrees. In the past, he says, councils have been recognised as binding even when not all Churches have been able to be present. Nevertheless, it is "frustrating and scandalising" that some have chosen to withdraw.

He acknowledges that there are problems in the Orthodox world. However, he says, "if unity is the goal, you put everything aside for that. You come to a council because there are problems – but the way to meet those problems is at a council."

Furthermore, he says there was never any danger of smaller Churches being railroaded into decisions they didn't agree with. He points to the Orthodox principle of consensus, developed as a way of ensuring that the views of the smallest Churches were given exactly the same weight as those of the largest. In practice this means that for a decision to be adopted, everyone has to agree. Even the smallest Churches, he says, "have a vote that can overturn the majority. But you can't have a say in the consensus if you're away from the table. If Georgia [one of the Churches not attending] says no, consensus means you can't proceed. But you have to be at the table to do that."

Chryssavgis acknowledges the pain felt on both sides of the divide, including among those Churches that have said they will not attend. However, he says: "I would hope this council, with or without them, will take a first fragile step. We will be able to admire something beautiful. It will take time to see it, but it will be beautiful."

He maintains a certain optimism. However, for many observers the uncertainty and angst surrounding the council – and the absence of some Churches – marks a missed opportunity for reform and progress. Whatever the technical status of the council, the Churches that did not attend have given themselves an excuse of ignoring it. Years of careful preparations have been compromised at the eleventh hour by a bewildering outbreak of hostility and suspicion. Whether another such opportunity will present itself remains to be seen.

Follow Mark Woods on Twitter: @RevMarkWoods