Dr Rowan Williams said the absence of the Primates had been "felt and noted every day", and that the names of the missing Primates had been placed on seats in the meeting and candles lit for them.
In spite of their absence, Dr Williams said there was still a lot of solidarity between churches in the Communion on a broad range of issues and that the meeting had met his hope of clarifying the role of the Primates standing committee.
"Of course, there is a critical situation in the Communion. Nobody would deny that. But that critical situation has not ended relationships, often very cordial and constructive, between Churches within the Communion," he said.
The Archbishop said he had recently met some of those not present, including the Archbishop of Kenya, and that more meetings were planned with absent Primates.
"There is no suggestion that this is somehow closing the door on those who are not with us," he said.
The Archbishop expressed his hope in members of the Primates Standing Committee working to re-establish local and regional relationships, but acknowledged that it was a "long task".
"I've no crystal ball about the future. Clearly the division is very real. Nobody is denying that. The question is how we cope with it, how we argue with one another, whether we are still able to sit in the same room and argue the case, and that's why I'm sorry that there are not those here to continue that argument among us," he said.
With the likelihood of many parishes and individuals joining a new ordinariate in the Roman Catholic Church, the Archbishop admitted that the task of holding the Communion together was "difficult".
"It's the task we've been given. It's part of the gift of living in the Church. It's part of the cross we carry," he said.
However, the Archbishop questioned some reports suggesting that as many as 1,000 parishes and individuals in the UK are considering the move to Rome. He said the figure was "exaggerated" but wished those planning to join the ordinariate well.
"If this if for them a step further towards communion with Jesus Christ, God bless them. I can't go with them, I can't agree, but they are doing this in good faith and good conscience and why should I complain about that."
The Primates meeting ended with the release of several statements, including one condemning the murder last week of Ugandan gay rights activist David Kato.
Dr Williams said the murder "illustrates the fact that words have results".
"That is certainly a lesson we all need to learn whenever we use any kind of language that demonises or demeans such persons. We have to think: these are the possible consequences."
He defended the Archbishop of Uganda Henry Orombi, who was absent from the meeting, against the accusation that his opposition to homosexuality had been a factor in Kato's murder.
"He was a signatory along with all the other Primates in our statement today deploring and condemning all violence and demeaning language about homosexual persons," he said.
Several open letters were issued at the end of the meeting, including one committing Primates to addressing violence against women and girls in their provinces, and another calling upon Zimbabwean President Robert Mugabe to end the harassment of Anglican churches by authorities in Zimbabwe.