Services of remembrance are taking place at parish churches across the UK.
Liberal Christian research group Ekklesia says this amounts to the Church making a "political statement" at odds with its teaching and beliefs.
But the Rector of Putney said this "missed the point" and it was right to remember sacrifices made for others.
Ekklesia said it was not suggesting that the Church is celebrating British victories, even less that it is celebrating war itself.
But it does claim that, when the Church says it is commemorating "those who have given their lives for the peace and freedom we enjoy today", it is ignoring the political and theological implications of its actions.
Co-director Jonathan Bartley said: "There's a clear and present sentiment behind the poppies and the prayers - and one that, if the people in the pews really stopped to think about, would not be shared by all who attend (Remembrance Day) services."
"Many bishops and clergy certainly can't sign up wholeheartedly to the idea that those who died in the Falklands, Iraq, and even World War I, gave their lives for 'peace and freedom'.
"Some feel that the military campaigns worked against it."
In 2003, the Archbishop of Canterbury Rowan Williams joined forces with the leader of the Roman Catholic Church in England and Wales, Cardinal Cormac Murphy-O'Connor, to question the moral basis of the Iraq War.
Rev Dr Giles Fraser, the Rector of Putney in south-west London, said Ekklesia was missing the point.
"I think the Iraq war was wrong... but these aren't services in celebration of some cheap nationalism," he said.
"We are celebrating the service of people who put their lives on the line for others... and that's absolutely right and proper".
Difficult job
Dr Fraser - who lectures Army officers on the ethics of conflict - presided over a service of remembrance typical of those in other Anglican churches.
He received a military parade and then welcomed troops into St Mary's Church, in Putney, where their standards were placed behind the altar.
He said the Church of England's special position in the state allowed it to "articulate a spiritual and a moral side" to institutions such as the armed forces.
"They do a very difficult job... they don't get a lot of money, they don't get a lot of glory for doing it, they do it in the care for others. That's exactly right with my values as a Christian, and other people's too," he said.
Putney's local MP, Conservative Justine Greeening, who is a member of the congregation at St Mary's, said that global media was raising awareness of the suffering of people on all sides of conflict.
She said: "I think understanding how everyone gets involved is important, but we should start at home with remembering how our servicemen and women were affected."+++++++++++++++++++++++++++++++++++++++++++++++++++
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(Source: BBC)